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Crystal structure of an immunoreactive 32 kDa antigen PG49 (PG_0181) from Porphyromonas gingivalis W83 at 1.45 A resolution (PSI Community Target, Nakayama)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 0.17M sodium acetate, 15.0% Glycerol, 28.5% polyethylene glycol 4000, 4.0% Acetone, 0.1M TRIS pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.636 α = 90 b = 86.821 β = 90 c = 90.645 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 Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2014-07-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9184,0.9791 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 43.411 99.1 0.083 13.38 55908 -3 11.182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 98.3 0.714 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.45 43.411 55846 2833 99.14 0.1191 0.1171 0.1326 0.1569 0.1618 RANDOM 15.1539
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] 0.38 0.39 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_sphericity_free 29.418 r_dihedral_angle_4_deg 17.957 r_rigid_bond_restr 11.703 r_dihedral_angle_3_deg 10.897 r_sphericity_bonded 9.542 r_dihedral_angle_1_deg 6.415 r_mcangle_it 1.975 r_mcbond_it 1.729 r_mcbond_other 1.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_sphericity_free 29.418 r_dihedral_angle_4_deg 17.957 r_rigid_bond_restr 11.703 r_dihedral_angle_3_deg 10.897 r_sphericity_bonded 9.542 r_dihedral_angle_1_deg 6.415 r_mcangle_it 1.975 r_mcbond_it 1.729 r_mcbond_other 1.728 r_angle_refined_deg 1.605 r_angle_other_deg 0.779 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2383 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 56
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing