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Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 300-350 mM NaCl, 21-24% methyl ether poly(ethylene glycol) 5000, buffered with 100 mM triethanolamine (pH 8.0 at 25 C). , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.868 α = 90 b = 104.058 β = 104.37 c = 78.254 γ = 90
Symmetry Space Group P 1 21 1
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 2005-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.964108 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 1.97 75.81 98.2 0.029 21.1 1.9 204015
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 1.97 2.02 95.5 0.074 9.1 1.7 3643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.97 75.81 53215 2850 98.65 0.15937 0.15788 0.1597 0.18769 0.1909 RANDOM 14.034
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] -0.2 -0.28 0.3 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.272 r_dihedral_angle_4_deg 14.276 r_dihedral_angle_3_deg 11.853 r_dihedral_angle_1_deg 5.361 r_scangle_it 1.775 r_scbond_it 1.109 r_angle_refined_deg 1.073 r_mcangle_it 0.717 r_mcbond_it 0.433 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.272 r_dihedral_angle_4_deg 14.276 r_dihedral_angle_3_deg 11.853 r_dihedral_angle_1_deg 5.361 r_scangle_it 1.775 r_scbond_it 1.109 r_angle_refined_deg 1.073 r_mcangle_it 0.717 r_mcbond_it 0.433 r_nbtor_refined 0.301 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5649 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing