5PEB

PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 104)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727730% PEG600 -- 0.1M MES pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.7367

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.857α = 90
b = 97.662β = 90
c = 58.578γ = 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
12.1129.2998.60.1130.1230.0480.99811.76.414083
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)
12.112.17860.8510.9360.3810.8015.4995

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 SYNTHESISTHROUGHOUT3G0L2.1129.291336570698.450.19220.18960.2399RANDOM39.887
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]
2.63-1.78-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.401
r_dihedral_angle_4_deg21.53
r_dihedral_angle_3_deg12.938
r_dihedral_angle_1_deg5.91
r_mcangle_it5.764
r_mcbond_it4.136
r_mcbond_other4.099
r_angle_refined_deg1.969
r_angle_other_deg1.075
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.401
r_dihedral_angle_4_deg21.53
r_dihedral_angle_3_deg12.938
r_dihedral_angle_1_deg5.91
r_mcangle_it5.764
r_mcbond_it4.136
r_mcbond_other4.099
r_angle_refined_deg1.969
r_angle_other_deg1.075
r_chiral_restr0.112
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.001
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