☰ Navigation Tabs
Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoformate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SZY PDB ENTRY 3SZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.637 α = 90 b = 111.637 β = 90 c = 72.506 γ = 90
Symmetry Space Group P 43 21 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 MARMOSAIC 300 mm CCD 2010-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 1.6 50 99.3 0.08 8.4 11.3 60520
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 1.6 1.66 96.4 0.38 9 5778
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3SZY 1.6 25 60399 3062 99.36 0.1946 0.1934 0.1924 0.2162 0.2159 RANDOM 17.7883
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 13.206 r_dihedral_angle_3_deg 12.146 r_dihedral_angle_1_deg 5.253 r_scangle_it 2.161 r_scbond_it 1.263 r_angle_refined_deg 1.079 r_mcangle_it 0.923 r_mcbond_it 0.491 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 13.206 r_dihedral_angle_3_deg 12.146 r_dihedral_angle_1_deg 5.253 r_scangle_it 2.161 r_scbond_it 1.263 r_angle_refined_deg 1.079 r_mcangle_it 0.923 r_mcbond_it 0.491 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MD2 data collection PHASER phasing