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Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys-gingipain (Kgp)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 2.0M Ammonium sulfate, 0.2M Ammonium nitrate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.911 α = 90 b = 59.858 β = 94.23 c = 85.672 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 2008-07-15 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-02-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95667 Australian Synchrotron MX1 2 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97949, 0.97962, 0.94947 APS 23-ID-B
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 1,2 1.4 17 94.8 0.058 11.8 3.6 56082
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) 1.4 1.42 96 0.266 3.6 2864
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 1.4 15.32 56068 2829 94.7 0.177 0.175 0.1812 0.208 0.2152 RANDOM 14.589
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] -0.67 -0.06 0.79 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.258 r_dihedral_angle_4_deg 13.482 r_dihedral_angle_3_deg 11.145 r_dihedral_angle_1_deg 7.915 r_scangle_it 4.016 r_scbond_it 2.979 r_mcangle_it 2.461 r_mcbond_it 1.773 r_angle_refined_deg 1.492 r_angle_other_deg 0.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.258 r_dihedral_angle_4_deg 13.482 r_dihedral_angle_3_deg 11.145 r_dihedral_angle_1_deg 7.915 r_scangle_it 4.016 r_scbond_it 2.979 r_mcangle_it 2.461 r_mcbond_it 1.773 r_angle_refined_deg 1.492 r_angle_other_deg 0.867 r_mcbond_other 0.601 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2646 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling SHELXCD phasing SHELXE model building