5PBU

PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 15)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727730% PEG600 -- 0.1M MES pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.6366.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.03α = 90
b = 96.896β = 90
c = 58.021γ = 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
11.8829.0198.60.0830.090.0350.998136.419085
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)
11.881.9282.40.9941.0890.4360.6915.71016

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 SYNTHESISTHROUGHOUT3G0L1.8829.011812394698.770.18480.1830.2198RANDOM34.683
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]
2.66-1.12-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.157
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg12.239
r_dihedral_angle_1_deg5.646
r_mcangle_it4.449
r_mcbond_other3.316
r_mcbond_it3.312
r_angle_refined_deg1.9
r_angle_other_deg1.038
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.157
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg12.239
r_dihedral_angle_1_deg5.646
r_mcangle_it4.449
r_mcbond_other3.316
r_mcbond_it3.312
r_angle_refined_deg1.9
r_angle_other_deg1.038
r_chiral_restr0.105
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d0.003
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