☰ Navigation Tabs
Structure of the YPO2259 putative oxidoreductase from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 35% Tacsimate, 10mM magnesium chloride, 100mM HEPES, 300mM NDSB-195, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.55 α = 90 b = 97.55 β = 90 c = 172.51 γ = 120
Symmetry Space Group P 65 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 110 CCD MARMOSAIC 225 mm CCD beryllium lens 2009-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.75 50 99.4 0.098 8.3 6.3 13362 13282 1.8 3.2
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 2.75 2.85 99.8 0.616 3.2 6.6 1267
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 SAD THROUGHOUT 2.75 46.93 3.2 13314 13251 655 99.53 0.2 0.2 0.199 0.2019 0.245 0.2476 RANDOM 22.948
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] -0.23 -0.12 -0.23 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 14.272 r_dihedral_angle_4_deg 11.63 r_scangle_it 6.026 r_dihedral_angle_1_deg 4.941 r_scbond_it 3.91 r_mcangle_it 2.503 r_mcbond_it 1.344 r_angle_refined_deg 0.796 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 14.272 r_dihedral_angle_4_deg 11.63 r_scangle_it 6.026 r_dihedral_angle_1_deg 4.941 r_scbond_it 3.91 r_mcangle_it 2.503 r_mcbond_it 1.344 r_angle_refined_deg 0.796 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2700 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BLU-MAX data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing