5PBM

PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 7)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727730% PEG600 -- 0.1M MES pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.5765.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.03α = 90
b = 96.69β = 90
c = 57.889γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-03-10SINGLE 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
11.6728.9499.70.0430.0470.0181226.627024
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)
11.671.794.70.860.940.3730.87161294

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 SYNTHESISTHROUGHOUT3G0L1.6728.9425663134299.540.18480.18360.2091RANDOM35.22
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]
3.66-1.57-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.874
r_dihedral_angle_4_deg20.787
r_dihedral_angle_3_deg12.243
r_dihedral_angle_1_deg6.114
r_mcangle_it4.774
r_mcbond_it3.695
r_mcbond_other3.693
r_angle_refined_deg2.23
r_angle_other_deg1.135
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.874
r_dihedral_angle_4_deg20.787
r_dihedral_angle_3_deg12.243
r_dihedral_angle_1_deg6.114
r_mcangle_it4.774
r_mcbond_it3.695
r_mcbond_other3.693
r_angle_refined_deg2.23
r_angle_other_deg1.135
r_chiral_restr0.133
r_bond_refined_d0.028
r_gen_planes_refined0.012
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms930
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing