4LC2 | pdb_00004lc2

Crystal structure of the bromodomain of human BRPF1B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DVV	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	1X0J	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3DAI	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3HMH	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2GRC	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2OO1	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2OSS	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	2OUO	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3D7C	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental model	PDB	3DWY	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	277	20% PEG3350 0.1 M bis tris propane, 10% ethylene glycol 0.15 M sodium nitrate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.835	α = 90
b = 60.835	β = 90
c = 63.679	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	RIGAKU RAXIS IV		2013-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.65	19	99.7	0.026	0.026	40.1	6.7	16843	16793			20.6

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	1.65	1.74	98.3		0.135	0.135	5.8	5.5	2379

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY	1.65	19	16838	16767	847	99.58	0.1767	0.1767	0.1744	0.19	0.2198	0.23	RANDOM	25.5295

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]
-0.19	-0.19		-0.19		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.042
r_dihedral_angle_4_deg	18.127
r_dihedral_angle_3_deg	13.125
r_mcangle_it	5.662
r_mcbond_it	4.922
r_dihedral_angle_1_deg	4.755
r_mcbond_other	4.651
r_angle_refined_deg	1.615
r_angle_other_deg	0.883
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	936
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	8

Software

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