3RCW | pdb_00003rcw

Crystal Structure of the bromodomain of human BRD1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HME	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2MB3	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OSS	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OIO	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2GRC	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OO1	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DAI	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3D7C	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DWY	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	277	32.5% PEG3350, 5% EtGly, 0.1M Acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.137	α = 100.61
b = 51.245	β = 90.75
c = 130.626	γ = 93.89

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2011-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.0000	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.21	19.892	96.7	0.057	0.057	9.6	2	54956	53142			39.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.33	96.8		0.418	0.418	1.9	2.1	7768

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY	2.21	19.85	54860	53137	1999	96.86	0.2087	0.2087	0.2061	0.21	0.2751	0.27	RANDOM	41.3436

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
3.23	-0.7	0.95	-1.75	-1.3	-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.915
r_dihedral_angle_4_deg	18.004
r_dihedral_angle_3_deg	16.296
r_scangle_it	12.608
r_scbond_it	10.258
r_mcangle_it	6.238
r_dihedral_angle_1_deg	5.424
r_mcbond_it	4.442
r_mcbond_other	1.463
r_angle_refined_deg	1.43
r_angle_other_deg	0.902
r_chiral_restr	0.074
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7216
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	23

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction