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1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine
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, SITTING DROP 293 0.8 M Sodium potassium tartrate
20% (w/v) PEG 3350
5 mM Arginine
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.165 α = 90 b = 149.129 β = 90 c = 245.089 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 RAYONIX MX300-HS 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-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 2.3 50 99.5 0.074 0.074 22.7 7.9 53084 -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 2.3 2.34 98.2 0.766 0.871 1.6 7.5
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 2.3 50 50360 2686 99.38 0.18701 0.18553 0.1874 0.21469 0.2156 RANDOM 66.277
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] 3.35 -1.65 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.222 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 13.639 r_long_range_B_refined 6.124 r_long_range_B_other 6.124 r_dihedral_angle_1_deg 5.431 r_scangle_other 3.829 r_angle_other_deg 3.715 r_mcangle_it 2.845 r_mcangle_other 2.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.222 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 13.639 r_long_range_B_refined 6.124 r_long_range_B_other 6.124 r_dihedral_angle_1_deg 5.431 r_scangle_other 3.829 r_angle_other_deg 3.715 r_mcangle_it 2.845 r_mcangle_other 2.845 r_scbond_it 2.332 r_scbond_other 2.332 r_mcbond_it 1.735 r_mcbond_other 1.731 r_angle_refined_deg 1.392 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 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 5904 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing