☰ Navigation Tabs
Structure of a domain of an uncharacterized protein PG_1388 from Porphyromonas gingivalis W83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.2M Ammonium acetate, 0.1M BIS-TRIS pH 6.5, 25 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.753 α = 86.55 b = 48.259 β = 79.58 c = 54.191 γ = 68.35
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 mirrors 2007-02-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924, 0.97938 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 1.76 35 92.9 0.07 14.4 3.5 37374 37374 27.2
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 1.76 1.79 71.7 0.19 6 3.2
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 MAD THROUGHOUT 1.76 35 35455 35455 1873 92.89 0.16849 0.16547 0.172 0.22645 0.2353 RANDOM 9.885
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] 0.56 -0.27 -0.38 0.33 0.41 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.31 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 12.458 r_dihedral_angle_1_deg 6.187 r_scangle_it 2.784 r_scbond_it 2.049 r_angle_refined_deg 1.566 r_mcangle_it 1.195 r_angle_other_deg 0.936 r_mcbond_it 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.31 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 12.458 r_dihedral_angle_1_deg 6.187 r_scangle_it 2.784 r_scbond_it 2.049 r_angle_refined_deg 1.566 r_mcangle_it 1.195 r_angle_other_deg 0.936 r_mcbond_it 0.93 r_symmetry_vdw_other 0.282 r_mcbond_other 0.26 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.208 r_nbd_other 0.208 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.167 r_chiral_restr 0.092 r_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3183 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 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