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Structure of the transporter associated domain from PG_0272, a CBS domain protein from Porphyromonas gingivalis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 291 0.1M citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.03 39.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.733 α = 90 b = 45.195 β = 90 c = 57.214 γ = 90
Symmetry Space Group P 21 21 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 CUSTOM-MADE 2006-10-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97910, 0.97929 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.3 24.2 94.6 0.068 11.6 7.8 20972 20972 -3 16.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 69 0.264 3.6 3.6
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 1.3 24.17 19898 19898 1072 94.63 0.13157 0.13157 0.12978 0.1286 0.16715 0.1655 RANDOM 15.998
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] 1.31 -0.71 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.537 r_dihedral_angle_3_deg 10.925 r_dihedral_angle_4_deg 10.869 r_sphericity_free 7.207 r_dihedral_angle_1_deg 6.415 r_scangle_it 4.834 r_sphericity_bonded 4.655 r_scbond_it 3.381 r_mcangle_it 2.196 r_rigid_bond_restr 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.537 r_dihedral_angle_3_deg 10.925 r_dihedral_angle_4_deg 10.869 r_sphericity_free 7.207 r_dihedral_angle_1_deg 6.415 r_scangle_it 4.834 r_sphericity_bonded 4.655 r_scbond_it 3.381 r_mcangle_it 2.196 r_rigid_bond_restr 2.022 r_mcbond_it 1.712 r_angle_refined_deg 1.601 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.27 r_symmetry_hbond_refined 0.262 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 709 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 12
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