3GG3 | pdb_00003gg3

Crystal Structure of the Bromodomain of Human PCAF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NXB	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OO1	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OSS	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OUO	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2RFJ	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	3DAI	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	277	20% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.226	α = 90
b = 99.226	β = 90
c = 101.137	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2008-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5

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	2.25	32.743	100	0.048	0.048	12.5	2.8	17604	17604

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	2.25	2.37	100		0.456	0.456	2	2.8	2567

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	PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI	2.25	32.74	17610	17594	892	99.91	0.209	0.209	0.207	0.19	0.245	0.22	RANDOM	31.265

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]
-0.66	-0.33		-0.66		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.425
r_dihedral_angle_4_deg	22.367
r_dihedral_angle_3_deg	14.16
r_scangle_it	11.709
r_scbond_it	9.302
r_dihedral_angle_1_deg	5.605
r_mcangle_it	5.521
r_mcbond_it	3.906
r_angle_refined_deg	1.42
r_mcbond_other	1.25
r_angle_other_deg	0.903
r_chiral_restr	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1728
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction