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Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys-gingipain (Kgp) from Porphyromonas gingivalis w83
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KM5 PDB ENTRY 3KM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M Calcium acetate, 30% PEG 8000, 0.1M Na cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.251 α = 90 b = 123.131 β = 91.25 c = 62.614 γ = 90
Symmetry Space Group P 1 21 1
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 210r 2009-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95663 Australian Synchrotron MX1
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 1.56 50 96.7 0.032 19.1 2.4 89782 15.1
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 1.56 1.59 73.2 0.161 2.2 3401
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3KM5 1.56 23.24 89740 4535 97.29 0.159 0.158 0.191 0.2142 RANDOM 18.413
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] -0.24 -0.31 -1.14 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_dihedral_angle_4_deg 12.599 r_dihedral_angle_3_deg 9.273 r_dihedral_angle_1_deg 7.281 r_scangle_it 4.652 r_scbond_it 3.327 r_mcangle_it 2.758 r_mcbond_it 1.923 r_angle_refined_deg 1.551 r_angle_other_deg 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_dihedral_angle_4_deg 12.599 r_dihedral_angle_3_deg 9.273 r_dihedral_angle_1_deg 7.281 r_scangle_it 4.652 r_scbond_it 3.327 r_mcangle_it 2.758 r_mcbond_it 1.923 r_angle_refined_deg 1.551 r_angle_other_deg 0.934 r_mcbond_other 0.651 r_chiral_restr 0.092 r_bond_refined_d 0.013 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 5240 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling