7AV9

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in 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	3MB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20% PEG8000, 0.04M potassium phosphate monobasic

Crystal Properties
Matthews coefficient	Solvent content
2	38.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.49	α = 90
b = 27.02	β = 100.5
c = 55.94	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 2M		2015-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9173	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.23	14.51	96.9	0.997	22.9	2.9		34009

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.25			0.987

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3MB3	1.23	14.51	34009	1635	96.531	0.119	0.1179	0.146	14.779

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]
-0.293		-0.597	2.821		-2.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.364
r_dihedral_angle_3_deg	11.717
r_dihedral_angle_4_deg	10.94
r_dihedral_angle_1_deg	5.506
r_rigid_bond_restr	4.503
r_lrange_it	4.078
r_lrange_other	3.54
r_scangle_it	3.369
r_scangle_other	3.367
r_scbond_it	2.817
r_scbond_other	2.815
r_mcangle_other	2.055
r_mcangle_it	2
r_mcbond_it	1.895
r_angle_refined_deg	1.885
r_angle_other_deg	1.72
r_mcbond_other	1.623
r_nbd_refined	0.25
r_nbd_other	0.204
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.195
r_symmetry_xyhbond_nbd_refined	0.185
r_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.165
r_chiral_restr	0.117
r_symmetry_nbtor_other	0.089
r_xyhbond_nbd_other	0.076
r_bond_refined_d	0.015
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	1025
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	20

Software

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