☰ Navigation Tabs
Crystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 20% 1,4 butanediol, 0.1 imidazole pH 8.0, 0.1 M Zn(oAC)2, 0.1M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.961 α = 90 b = 84.826 β = 90 c = 164.535 γ = 90
Symmetry Space Group C 2 2 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 315 2006-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9795 APS 19-ID
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 2.01 40 99.5 0.095 15.1 3.5 35653 35476
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 2.01 2.08 97.5 0.466 2 2.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.01 40 37345 35476 1869 99.5 0.19094 0.18825 0.1886 0.24365 0.245 RANDOM 26.528
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] -2.47 2.12 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.399 r_dihedral_angle_4_deg 21.695 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_1_deg 6.142 r_scangle_it 3.129 r_scbond_it 2.027 r_angle_refined_deg 1.621 r_mcangle_it 1.161 r_mcbond_it 0.851 r_symmetry_hbond_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.399 r_dihedral_angle_4_deg 21.695 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_1_deg 6.142 r_scangle_it 3.129 r_scbond_it 2.027 r_angle_refined_deg 1.621 r_mcangle_it 1.161 r_mcbond_it 0.851 r_symmetry_hbond_refined 0.312 r_nbtor_refined 0.291 r_symmetry_vdw_refined 0.266 r_xyhbond_nbd_refined 0.25 r_nbd_refined 0.207 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3822 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing Coot model building CCP4 phasing