4J1P

X-ray crystal structure of bromodomain 2 of human brd2 in complex with rvx208 to 1.08 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ONIPDB ENTRY 3ONI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.329825% (w/v) PEG 1500, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.1α = 90
b = 66.35β = 90
c = 75.854γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.085099.60.04310.34.65566755428
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.081.1299.90.3884.55506

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ONI1.0819.565567955278281399.280.12950.12790.1592RANDOM15.8182
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]
-0.14-0.520.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.027
r_dihedral_angle_4_deg28.88
r_sphericity_free28.105
r_dihedral_angle_3_deg13.204
r_sphericity_bonded10.952
r_rigid_bond_restr7.209
r_dihedral_angle_1_deg6.71
r_angle_refined_deg2.402
r_angle_other_deg1.202
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.027
r_dihedral_angle_4_deg28.88
r_sphericity_free28.105
r_dihedral_angle_3_deg13.204
r_sphericity_bonded10.952
r_rigid_bond_restr7.209
r_dihedral_angle_1_deg6.71
r_angle_refined_deg2.402
r_angle_other_deg1.202
r_chiral_restr0.145
r_bond_refined_d0.027
r_gen_planes_refined0.018
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms938
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms31

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling