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The structure of putative dihydroorotase from Porphyromonas gingivalis.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 2M ammonium sulfate, 0.1M Cacodylate pH6.5, 0.1M NaCl, glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.459 α = 90 b = 86.873 β = 90 c = 114.581 γ = 90
Symmetry Space Group I 2 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 CUSTOM-MADE 2005-12-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97874, 0.97912 APS 19-BM
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 1.85 28.1 99.4 36917 36917
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 1.85 1.94 99 3.4 2.6
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 1.85 28.1 36917 35062 1855 99.4 0.15099 0.15099 0.14875 0.148 0.19372 0.1929 RANDOM 17.49
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] -0.06 0.81 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.145 r_dihedral_angle_4_deg 15.769 r_dihedral_angle_3_deg 13.914 r_dihedral_angle_1_deg 6.565 r_scangle_it 3.354 r_scbond_it 2.234 r_angle_refined_deg 1.379 r_mcangle_it 1.221 r_mcbond_it 0.826 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.145 r_dihedral_angle_4_deg 15.769 r_dihedral_angle_3_deg 13.914 r_dihedral_angle_1_deg 6.565 r_scangle_it 3.354 r_scbond_it 2.234 r_angle_refined_deg 1.379 r_mcangle_it 1.221 r_mcbond_it 0.826 r_nbtor_refined 0.304 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.1 r_metal_ion_refined 0.064 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3531 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling HKL-3000 phasing SHELX phasing CCP4 phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing O model building ARP/wARP model building Coot model building