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Pectin methylesterase from Yersinia enterocolitica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJV PDB ENTRY 1QJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 4.0 M sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.26 76.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.64 α = 90 b = 170.64 β = 90 c = 170.64 γ = 90
Symmetry Space Group P 43 3 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 ADSC QUANTUM 4r 2007-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.1 NSLS X8C
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 3.5 39.147 99.9 0.17 21.2 24.7 10653
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 3.5 3.69 99.9 0.6 5.9 21.1
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 1QJV 3.5 39.147 10653 530 99.65 0.19762 0.19527 0.1926 0.245 0.2406 RANDOM 57.949
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]
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.195 r_dihedral_angle_2_deg 36.722 r_sphericity_bonded 20.706 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_3_deg 15.549 r_dihedral_angle_1_deg 4.845 r_rigid_bond_restr 1.162 r_angle_refined_deg 0.924 r_chiral_restr 0.061 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.195 r_dihedral_angle_2_deg 36.722 r_sphericity_bonded 20.706 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_3_deg 15.549 r_dihedral_angle_1_deg 4.845 r_rigid_bond_restr 1.162 r_angle_refined_deg 0.924 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2412 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling