5S8Q | pdb_00005s8q

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with FMO3D000185a (space group P212121)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M HEPES pH 7.5 -- 0.1M calcium chloride -- 34% PEG3350 -- 4% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.06	α = 90
b = 55.99	β = 90
c = 91.76	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		2018-10-20		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96859	Diamond	I24

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	1.5	47.06	99.5	0.116	0.126	0.048	0.997	8.3	6.8		39433

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	1.5	1.54	98		1.126	1.238	0.504	0.544		5.6	2834

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	3MB3	1.5	41.91	37337	2033	99.4	0.1823	0.1789	0.18	0.2419	0.25	RANDOM	24.533

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]
-0.9			-2.03		2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.346
r_dihedral_angle_4_deg	19.224
r_dihedral_angle_3_deg	14.59
r_rigid_bond_restr	6.416
r_dihedral_angle_1_deg	6.17
r_mcangle_it	4.308
r_mcbond_it	3.658
r_mcbond_other	3.657
r_angle_refined_deg	1.837
r_angle_other_deg	1.603

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.346
r_dihedral_angle_4_deg	19.224
r_dihedral_angle_3_deg	14.59
r_rigid_bond_restr	6.416
r_dihedral_angle_1_deg	6.17
r_mcangle_it	4.308
r_mcbond_it	3.658
r_mcbond_other	3.657
r_angle_refined_deg	1.837
r_angle_other_deg	1.603
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2002
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	48

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.