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PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 103)
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 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.86 α = 90 b = 45.44 β = 102.02 c = 83.6 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 1.54 31.47 94.8 0.047 0.055 0.029 0.999 13.6 3.5 65960
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 1.54 1.58 89.4 0.63 0.746 0.394 0.703 3.5 4557
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 1.54 31.47 62654 3301 94.4 0.1723 0.1709 0.18 0.1994 0.2087 RANDOM 30.029
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] -0.85 0.23 0.17 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.847 r_dihedral_angle_4_deg 15.55 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_1_deg 6.282 r_mcangle_it 5.436 r_mcbond_it 3.49 r_mcbond_other 3.487 r_angle_refined_deg 2.097 r_angle_other_deg 1.132 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.847 r_dihedral_angle_4_deg 15.55 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_1_deg 6.282 r_mcangle_it 5.436 r_mcbond_it 3.49 r_mcbond_other 3.487 r_angle_refined_deg 2.097 r_angle_other_deg 1.132 r_chiral_restr 0.143 r_bond_refined_d 0.025 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