5XHK | pdb_00005xhk

Crystal structure of the BRD2-BD2 in complex with phenanthridinone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IG6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25% PEG MME 2000, 10% Glycerol, Tris-Cl

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.04	α = 90
b = 52.51	β = 90
c = 71.37	γ = 90

Symmetry
Space Group	P 2 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	CCD	MARMOSAIC 225 mm CCD		2016-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.28	42.296	83.2	0.054	0.063	0.032	0.998	11.7	3.3		25998			9.08

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.28	1.35	88		0.291	0.291	0.351	0.192	0.89	2.5	3

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	MOLECULAR REPLACEMENT	THROUGHOUT	5IG6	1.28	20	24672	1280	82.4	0.1587	0.157	0.1586	0.1919	0.1923	RANDOM	13.542

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			-0.38		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.632
r_dihedral_angle_4_deg	19.602
r_sphericity_free	14.41
r_dihedral_angle_3_deg	12.271
r_sphericity_bonded	5.748
r_dihedral_angle_1_deg	4.499
r_rigid_bond_restr	1.207
r_angle_refined_deg	1.179
r_chiral_restr	0.083
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	941
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling