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PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 163)
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 3.6 65.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.502 α = 90 b = 96.72 β = 90 c = 58.056 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 29.03 97.9 0.064 0.07 0.028 0.999 13.8 5.6 24562
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 78.1 0.684 0.837 0.47 0.531 2.5 997
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 29.03 23327 1219 97.79 0.1951 0.1936 0.2035 0.2243 0.2334 RANDOM 34.081
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] 2.7 -1.18 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_4_deg 19.899 r_dihedral_angle_3_deg 12.251 r_dihedral_angle_1_deg 6.077 r_mcangle_it 4.728 r_mcbond_it 3.656 r_mcbond_other 3.653 r_angle_refined_deg 2.005 r_angle_other_deg 1.101 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_4_deg 19.899 r_dihedral_angle_3_deg 12.251 r_dihedral_angle_1_deg 6.077 r_mcangle_it 4.728 r_mcbond_it 3.656 r_mcbond_other 3.653 r_angle_refined_deg 2.005 r_angle_other_deg 1.101 r_chiral_restr 0.12 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.005 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