3MB3

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HMH	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	2NXB	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OO1	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OSS	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OUO	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	2RFJ	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DAI	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	3D7C	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DWY	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	11% PEG3350 4% glycerol,0.1M acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.09	α = 90
b = 92.09	β = 90
c = 76.12	γ = 120

Symmetry
Space Group	P 31 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				2010-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9762	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.25	39.88	99.7	0.081	0.081	9.2	3.6	18066	18012			41.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.37	99.8		0.453	0.53	2	3.7	2602

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY	2.25	39.88	18065	17988	914	99.57	0.208	0.208	0.206	0.257	RANDOM	55.905

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]
3.37	1.69		3.37		-5.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.072
r_dihedral_angle_3_deg	15.678
r_scangle_it	14.065
r_dihedral_angle_4_deg	13.709
r_scbond_it	11.001
r_mcangle_it	6.428
r_dihedral_angle_1_deg	5.861
r_mcbond_it	4.49
r_angle_other_deg	1.946
r_angle_refined_deg	1.573

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.072
r_dihedral_angle_3_deg	15.678
r_scangle_it	14.065
r_dihedral_angle_4_deg	13.709
r_scbond_it	11.001
r_mcangle_it	6.428
r_dihedral_angle_1_deg	5.861
r_mcbond_it	4.49
r_angle_other_deg	1.946
r_angle_refined_deg	1.573
r_mcbond_other	1.306
r_chiral_restr	0.078
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	941
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	7

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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.