5R4X | pdb_00005r4x

XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13413a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	2.2M ammonium sulfate, 0.1M bis-tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.79	α = 90
b = 80.79	β = 90
c = 140.36	γ = 120

Symmetry
Space Group	P 65 2 2

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	DECTRIS PILATUS 6M		2015-11-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.4	70.18	100	0.07	0.072	0.017	1	24.8	17.5		53979

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.44	99.9		2.034	2.124	0.603	0.471		12.2	3908

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	FOURIER SYNTHESIS	THROUGHOUT	3DAI	1.4	49.6	51181	2720	99.94	0.1332	0.1319	0.13	0.1589	0.16	RANDOM	23.542

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]
0.28	0.14		0.28		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.584
r_dihedral_angle_4_deg	16.001
r_dihedral_angle_3_deg	11.802
r_dihedral_angle_1_deg	4.629
r_rigid_bond_restr	4.116
r_mcangle_it	3.22
r_mcbond_it	2.649
r_mcbond_other	2.649
r_angle_refined_deg	1.888
r_angle_other_deg	1.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.584
r_dihedral_angle_4_deg	16.001
r_dihedral_angle_3_deg	11.802
r_dihedral_angle_1_deg	4.629
r_rigid_bond_restr	4.116
r_mcangle_it	3.22
r_mcbond_it	2.649
r_mcbond_other	2.649
r_angle_refined_deg	1.888
r_angle_other_deg	1.523
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1084
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.