5PGC

PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 176)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727730% PEG600 -- 0.1M MES pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.5665.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.56α = 90
b = 96.618β = 90
c = 58.117γ = 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
11.6129.0693.50.070.0770.0310.99811.65.227949
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)
11.611.6454.50.660.8140.4650.4622.1769

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 SYNTHESISTHROUGHOUT3G0L1.6129.0626532140093.310.190.18830.2227RANDOM32.343
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]
3.96-1.51-2.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.115
r_dihedral_angle_4_deg16.911
r_dihedral_angle_3_deg11.733
r_dihedral_angle_1_deg5.465
r_mcangle_it4.218
r_mcbond_it3.154
r_mcbond_other3.134
r_angle_refined_deg1.967
r_angle_other_deg1.145
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.115
r_dihedral_angle_4_deg16.911
r_dihedral_angle_3_deg11.733
r_dihedral_angle_1_deg5.465
r_mcangle_it4.218
r_mcbond_it3.154
r_mcbond_other3.134
r_angle_refined_deg1.967
r_angle_other_deg1.145
r_chiral_restr0.117
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.01
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