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1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M Sodium citrate pH 5.0, 0.8 M Ammonium phosphate, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.34 63.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.063 α = 90 b = 149.247 β = 90 c = 243.768 γ = 90
Symmetry Space Group C 2 2 21
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 315r 2013-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97912 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 99.2 0.051 0.051 31 6 46042 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 92.4 0.402 0.934 2.7 5.4
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 FOURIER SYNTHESIS THROUGHOUT 5KQO 2.4 50 43578 2274 99.16 0.19077 0.18875 0.1916 0.22883 0.2296 RANDOM 88.721
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] 6.43 -2.97 -3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.886 r_dihedral_angle_3_deg 14.119 r_dihedral_angle_4_deg 13.978 r_long_range_B_refined 10.799 r_long_range_B_other 10.799 r_scangle_other 8.311 r_mcangle_it 6.539 r_mcangle_other 6.539 r_scbond_it 6.008 r_dihedral_angle_1_deg 5.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.886 r_dihedral_angle_3_deg 14.119 r_dihedral_angle_4_deg 13.978 r_long_range_B_refined 10.799 r_long_range_B_other 10.799 r_scangle_other 8.311 r_mcangle_it 6.539 r_mcangle_other 6.539 r_scbond_it 6.008 r_dihedral_angle_1_deg 5.52 r_scbond_other 5.466 r_mcbond_other 4.54 r_mcbond_it 4.539 r_angle_other_deg 3.629 r_angle_refined_deg 1.909 r_chiral_restr 0.113 r_bond_refined_d 0.02 r_gen_planes_other 0.014 r_gen_planes_refined 0.009 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5890 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing