5PPK

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 21)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M bis-tris pH 7.0 -- 30% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.442α = 90
b = 56.135β = 90
c = 101.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-08-28SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8729.0198.20.0770.0840.0320.99918.46.726525
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.9296.30.8380.9070.3430.8276.71884

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5AMF1.8729.0125249123497.90.18950.18740.2312RANDOM29.004
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]
2.55-0.44-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.512
r_dihedral_angle_4_deg13.595
r_dihedral_angle_3_deg13.11
r_dihedral_angle_1_deg5.091
r_mcangle_it3.465
r_mcbond_it2.611
r_mcbond_other2.606
r_angle_refined_deg1.669
r_angle_other_deg1.065
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.512
r_dihedral_angle_4_deg13.595
r_dihedral_angle_3_deg13.11
r_dihedral_angle_1_deg5.091
r_mcangle_it3.465
r_mcbond_it2.611
r_mcbond_other2.606
r_angle_refined_deg1.669
r_angle_other_deg1.065
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1953
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing