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PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z2856434854
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 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.487 α = 90 b = 116.712 β = 90 c = 147.406 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 6M 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 2.315 73.703 94.4 0.099 0.038 0.999 13.1 6.8 60855 55.65
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 2.315 2.497 57.8 1.258 0.469 0.702 7.1 3044
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 2.313 73.7 60858 3082 78.2 0.2148 0.2131 0.2192 0.2462 0.2497 RANDOM 50.85
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] 2.5801 -0.2896 -2.2905
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.25 t_omega_torsion 2.98 t_angle_deg 0.89 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.25 t_omega_torsion 2.98 t_angle_deg 0.89 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10951 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 39
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing