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PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 106)
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 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.9 α = 90 b = 45.57 β = 101.9 c = 83.68 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 1.59 31.29 90.8 0.042 0.049 0.025 0.999 17.9 3.7 57636
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 1.59 1.63 93.3 0.593 0.692 0.354 0.766 3.8 4342
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4PTB 1.59 31.29 54751 2880 90.31 0.1751 0.1734 0.2067 0.2116 RANDOM 32.004
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 0.35 0.32 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.311 r_dihedral_angle_4_deg 16.981 r_dihedral_angle_3_deg 12.856 r_dihedral_angle_1_deg 6.368 r_mcangle_it 5.426 r_mcbond_it 3.512 r_mcbond_other 3.51 r_angle_refined_deg 1.985 r_angle_other_deg 1.114 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.311 r_dihedral_angle_4_deg 16.981 r_dihedral_angle_3_deg 12.856 r_dihedral_angle_1_deg 6.368 r_mcangle_it 5.426 r_mcbond_it 3.512 r_mcbond_other 3.51 r_angle_refined_deg 1.985 r_angle_other_deg 1.114 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.003 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