5PVL | pdb_00005pvl

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 236)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1M bis-tris pH 7.0 -- 30% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.25	α = 90
b = 56.408	β = 90
c = 101.75	γ = 90

Symmetry
Space Group	P 21 21 21

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 2M		2014-08-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	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	1.53	21.69	98.5	0.066	0.073	0.03	0.999	13.3	5.7		47904

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	1.53	1.6	99.4		0.668	0.735	0.302	0.65		5.7	6331

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	5AMF	1.53	21.69	45496	2352	98.15	0.1945	0.1928	0.2	0.2284	0.23	RANDOM	22.106

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]
1.32			-0.67		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.305
r_dihedral_angle_4_deg	13.928
r_dihedral_angle_3_deg	13.512
r_dihedral_angle_1_deg	4.724
r_mcangle_it	2.902
r_mcbond_it	2.145
r_mcbond_other	2.138
r_angle_refined_deg	2.023
r_angle_other_deg	1.115
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.305
r_dihedral_angle_4_deg	13.928
r_dihedral_angle_3_deg	13.512
r_dihedral_angle_1_deg	4.724
r_mcangle_it	2.902
r_mcbond_it	2.145
r_mcbond_other	2.138
r_angle_refined_deg	2.023
r_angle_other_deg	1.115
r_chiral_restr	0.13
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1953
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	21

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.