7ZFY | pdb_00007zfy

BRD4 in complex with PepLite-Gly

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LRQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.896	α = 90
b = 43.531	β = 90
c = 79.967	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 6M		2019-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.911635	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	1.15	39.98	100	0.101	0.11	0.042	1	11.8	12.9		47837

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	1.15	1.17			3.299	3.578	1.374	0.371		13

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LRQ	1.15	39.98	47768	2333	99.967	0.198	0.1969	0.2	0.2133	0.21	18.007

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]
0.595			-0.548		-0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.696
r_dihedral_angle_4_deg	27.74
r_dihedral_angle_3_deg	12.73
r_lrange_it	6.94
r_dihedral_angle_1_deg	5.505
r_scangle_it	4.402
r_scbond_it	3.398
r_angle_refined_deg	1.969
r_mcangle_it	1.905
r_mcbond_it	1.272

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.696
r_dihedral_angle_4_deg	27.74
r_dihedral_angle_3_deg	12.73
r_lrange_it	6.94
r_dihedral_angle_1_deg	5.505
r_scangle_it	4.402
r_scbond_it	3.398
r_angle_refined_deg	1.969
r_mcangle_it	1.905
r_mcbond_it	1.272
r_symmetry_nbd_refined	0.357
r_nbtor_refined	0.321
r_xyhbond_nbd_refined	0.277
r_nbd_refined	0.238
r_symmetry_xyhbond_nbd_refined	0.219
r_chiral_restr	0.119
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1076
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
PHASER	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.