5PRG

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 88)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M bis-tris pH 7.0 -- 30% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1843.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.337α = 90
b = 56.41β = 90
c = 102.013γ = 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
12.6829.1297.40.0890.0990.0410.987276.29215
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)
12.682.7589.40.3020.3440.160.9635.1606

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 SYNTHESISTHROUGHOUT5AMF2.6829.12839343793.220.21590.21280.2731RANDOM12.673
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]
1.35-0.44-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.057
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg13.058
r_dihedral_angle_1_deg4.803
r_mcangle_it1.776
r_angle_refined_deg1.444
r_mcbond_it1.013
r_mcbond_other1.002
r_angle_other_deg0.963
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.057
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg13.058
r_dihedral_angle_1_deg4.803
r_mcangle_it1.776
r_angle_refined_deg1.444
r_mcbond_it1.013
r_mcbond_other1.002
r_angle_other_deg0.963
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.005
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