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Crystal structure of Apo PinO from Porphyromonas gingivitis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 25% PEG MED SMEAR
Crystal Properties Matthews coefficient Solvent content 2.18 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.254 α = 90 b = 54.102 β = 90 c = 161.091 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-F Mirrors 2017-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91787 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 2.458 80.546 97.5 0.135 0.147 0.135 0.997 0.147 6.4 14071 36.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.458 2.501 100 0.934 0.533 0.817 2 6.7
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 MOLECULAR REPLACEMENT THROUGHOUT 6EU8 2.46 80.546 13422 649 97.45 0.19595 0.19419 0.1939 0.23328 0.2327 RANDOM 42.19
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] -2.46 4.08 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.91 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 17.421 r_long_range_B_refined 7.655 r_dihedral_angle_1_deg 6.922 r_mcangle_it 4.276 r_scbond_it 3.454 r_mcbond_it 2.66 r_angle_refined_deg 1.223 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.91 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 17.421 r_long_range_B_refined 7.655 r_dihedral_angle_1_deg 6.922 r_mcangle_it 4.276 r_scbond_it 3.454 r_mcbond_it 2.66 r_angle_refined_deg 1.223 r_chiral_restr 0.092 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2935 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing