5S8I | pdb_00005s8i

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N01186d (space group C2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AV9	7AV9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	0.04M potassium phosphate monobasic -- 17% PEG8K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.073	α = 90
b = 27.433	β = 100.44
c = 56.717	γ = 90

Symmetry
Space Group	C 1 2 1

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		2016-06-23		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	1.3	55.78	99.1	0.028	0.034	0.019	0.999	19	3		31146

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	1.3	1.37	97.8		0.393	0.506	0.315	0.891		2.3	4453

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	7AV9	1.3	55.78	29454	1468	98.57	0.1675	0.1657	0.1744	0.2047	0.2207	RANDOM	20.474

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]
0.41		2.59	-0.47		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.272
r_dihedral_angle_4_deg	17.147
r_dihedral_angle_3_deg	12.192
r_dihedral_angle_1_deg	5.055
r_rigid_bond_restr	3.557
r_mcangle_it	2.317
r_mcbond_it	2.231
r_mcbond_other	1.973
r_angle_refined_deg	1.873
r_angle_other_deg	1.572
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	990
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	13

Software

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