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Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunoglobulin superfamily-like domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CVR PDB entry 1CVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 The best crystals were obtained at 20C with protein solution (at 5.7mg/mL in 5mM Tris HCl, pH 7.4, 0.02% sodium azide) and 22% polyethylene glycol 8000, 0.1M sodium cacodylate, pH 6.5, 0.2M calcium acetate as reservoir solution from 2:1 uL drops, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.64 α = 90 b = 58.81 β = 90 c = 135.5 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 CCD ADSC QUANTUM 315r 2012-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 1.75 45.2 99.5 0.1 16.5 6.6 46542 46309 22
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 1.75 1.79 93.9 0.692 1.9 3.4 3192
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1CVR 1.75 44.41 46504 46299 767 99.56 0.1496 0.1492 0.15 0.1722 0.1773 RANDOM 18.99
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] 0.8105 -0.5876 -0.2229
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.49 t_other_torsion 2.55 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.49 t_other_torsion 2.55 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3520 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 67
Software Software Software Name Purpose ADSC data collection PHASER phasing BUSTER refinement XDS data reduction XDS data scaling XSCALE data scaling