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1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex with Mn(2+)
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 5.5 293 0.1 M Sodium citrate pH 5.5, 0.8 M Ammonium phosphate, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.36 63.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.84 α = 90 b = 149.084 β = 90 c = 242.512 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 0.97915 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 2.5 50 93.4 0.092 0.092 16.9 5.3 38225 -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 2.5 2.54 91.3 0.367 0.917 2.9 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 2.5 50 32867 1722 84.1 0.19367 0.19172 0.1904 0.22997 0.2261 RANDOM 41.768
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] -0.66 -0.5 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.785 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 15.179 r_dihedral_angle_1_deg 5.843 r_long_range_B_refined 4.586 r_long_range_B_other 4.586 r_angle_other_deg 3.697 r_scangle_other 2.238 r_mcangle_it 1.896 r_mcangle_other 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.785 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 15.179 r_dihedral_angle_1_deg 5.843 r_long_range_B_refined 4.586 r_long_range_B_other 4.586 r_angle_other_deg 3.697 r_scangle_other 2.238 r_mcangle_it 1.896 r_mcangle_other 1.896 r_angle_refined_deg 1.677 r_scbond_it 1.325 r_scbond_other 1.325 r_mcbond_it 1.093 r_mcbond_other 1.092 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 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 5907 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing