3MB4

Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) with NMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G0JPDB entry 3G0J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.15M NaNO3 25% PEG 3350 10% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5251.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.957α = 90
b = 52.221β = 90
c = 134.964γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.665099.90.0670.064257.23607336037
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)RedundancyNumber Unique Reflections (All)
11.661.7299.80.9550.8171.976.63536

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3G0J1.6619.013592035898179599.940.1980.1980.1970.219RANDOM37.169
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]
1.75-0.68-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.209
r_dihedral_angle_4_deg16.528
r_dihedral_angle_3_deg13.335
r_scangle_it7.757
r_scbond_it6.561
r_dihedral_angle_1_deg4.991
r_mcangle_it3.655
r_mcbond_it2.6
r_angle_refined_deg1.473
r_angle_other_deg0.934
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.209
r_dihedral_angle_4_deg16.528
r_dihedral_angle_3_deg13.335
r_scangle_it7.757
r_scbond_it6.561
r_dihedral_angle_1_deg4.991
r_mcangle_it3.655
r_mcbond_it2.6
r_angle_refined_deg1.473
r_angle_other_deg0.934
r_mcbond_other0.886
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1896
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms38

Software

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