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PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 122)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0L 3G0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 30% PEG600 -- 0.1M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.62 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.616 α = 90 b = 96.89 β = 90 c = 58.179 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2013-03-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.72 29.09 99.2 0.053 0.057 0.022 0.999 18.4 6.5 25119
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) Redundancy Number Unique Reflections (All) 1 1.72 1.75 87.8 0.944 1.037 0.419 0.755 5.5 1240
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3G0L 1.72 29.09 23852 1251 99.18 0.1928 0.1913 0.2009 0.2204 0.2243 RANDOM 33.972
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] 2.81 -1.21 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 20.576 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_1_deg 5.636 r_mcangle_it 4.318 r_mcbond_other 3.376 r_mcbond_it 3.374 r_angle_refined_deg 2.018 r_angle_other_deg 1.092 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 20.576 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_1_deg 5.636 r_mcangle_it 4.318 r_mcbond_other 3.376 r_mcbond_it 3.374 r_angle_refined_deg 2.018 r_angle_other_deg 1.092 r_chiral_restr 0.116 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 930 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing