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PanDDA analysis group deposition of ground-state model of Porphyromonas gingivalis DPP11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JWF 5JWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 Morpheus Buffer system 1, 0.06M Divalents, 30% v/v Precipitant Mix 3
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.773 α = 90 b = 117.328 β = 90 c = 147.556 γ = 90
Symmetry Space Group P 21 21 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 2019-08-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.907 91.835 96.2 0.072 0.028 0.999 15.6 6.6 101212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.907 2.074 80.8 1.094 0.445 0.67 5.7 5061
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 5JWF 1.91 91.835 96027 5185 73.43 0.2148 0.2131 0.2195 0.2474 0.2534 RANDOM 37.635
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] 0.05 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.322 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 16.705 r_dihedral_angle_1_deg 7.244 r_mcangle_it 4.163 r_mcbond_it 2.936 r_mcbond_other 2.936 r_angle_refined_deg 1.558 r_angle_other_deg 1.365 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.322 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 16.705 r_dihedral_angle_1_deg 7.244 r_mcangle_it 4.163 r_mcbond_it 2.936 r_mcbond_other 2.936 r_angle_refined_deg 1.558 r_angle_other_deg 1.365 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10951 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing