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The structure of a predicted HAD-like family hydrolase from Porphyromonas gingivalis.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1.0 M K/Na tartrate, 0.1M Tris pH7.0, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.727 α = 90 b = 78.727 β = 90 c = 139.879 γ = 120
Symmetry Space Group P 62 2 2
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 315 2005-07-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979616, 0.97951 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 38.8 99.5 10573 10573 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 96.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.4 38.8 1573 10067 505 99.54 0.21271 0.21271 0.20948 0.2028 0.27583 0.2561 RANDOM 64.905
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] 1.68 0.84 1.68 -2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.863 r_dihedral_angle_4_deg 18.988 r_dihedral_angle_3_deg 18.859 r_dihedral_angle_1_deg 6.535 r_scangle_it 3.257 r_scbond_it 2.193 r_angle_refined_deg 1.484 r_mcangle_it 1.17 r_mcbond_it 0.912 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.863 r_dihedral_angle_4_deg 18.988 r_dihedral_angle_3_deg 18.859 r_dihedral_angle_1_deg 6.535 r_scangle_it 3.257 r_scbond_it 2.193 r_angle_refined_deg 1.484 r_mcangle_it 1.17 r_mcbond_it 0.912 r_nbtor_refined 0.306 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.205 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1659 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building