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PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 24)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PTB 4PTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1M MES pH 6.1 -- 20% PEG20K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.67 α = 90 b = 45.339 β = 102.12 c = 83.359 γ = 90
Symmetry Space Group C 1 2 1
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 2015-04-02 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 1.55 28.45 97.4 0.067 0.08 0.042 0.998 12.7 3.5 66241
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 1.55 1.59 94.6 0.764 0.91 0.487 0.644 3.4 4697
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 4PTB 1.55 28.45 62909 3332 96.98 0.1832 0.1818 0.1916 0.2096 0.2203 RANDOM 27.072
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] -1.01 0.43 0.23 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 6.398 r_mcangle_it 5.371 r_mcbond_it 3.369 r_mcbond_other 3.369 r_angle_refined_deg 2.053 r_angle_other_deg 1.138 r_chiral_restr 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 6.398 r_mcangle_it 5.371 r_mcbond_it 3.369 r_mcbond_other 3.369 r_angle_refined_deg 2.053 r_angle_other_deg 1.138 r_chiral_restr 0.152 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2925 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing