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Phosphopyruvate hydratase from Campylobacter jejuni.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PA6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.2 M magnesium chloride, 0.1 M imidazole buffer, 35% MPD, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.47 α = 90 b = 148.886 β = 90 c = 234.719 γ = 90
Symmetry Space Group I 2 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 100 CCD ADSC QUANTUM 210r 2009-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
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 2.13 35.9 98.7 0.096 10.4 5.8 115778 115778 42.9
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) 2.13 2.17 99.1 0.755 1.95 4.1 5734
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2PA6 2.13 35.9 113627 113627 5674 96.28 0.1781 0.1781 0.1761 0.1811 0.2159 0.2189 RANDOM 36.2297
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] 3.03 -1.28 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.726 r_dihedral_angle_4_deg 19.288 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_1_deg 6.077 r_scangle_it 3.701 r_scbond_it 2.33 r_angle_refined_deg 1.501 r_mcangle_it 1.393 r_angle_other_deg 0.973 r_mcbond_it 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.726 r_dihedral_angle_4_deg 19.288 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_1_deg 6.077 r_scangle_it 3.701 r_scbond_it 2.33 r_angle_refined_deg 1.501 r_mcangle_it 1.393 r_angle_other_deg 0.973 r_mcbond_it 0.788 r_mcbond_other 0.206 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12628 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 69
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing