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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, SITTING DROP 7 293 1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 3.4 63.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.356 α = 90 b = 149.853 β = 90 c = 246.008 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 MARMOSAIC 225 mm CCD 2014-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
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 99.9 0.07 0.07 21 8.1 53399 -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 99.8 0.668 0.859 2.1 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5KQO 2.3 50 50748 2571 99.93 0.18663 0.1847 0.22452 0.2028 RANDOM 49.587
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] 2.42 -2.21 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.862 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_3_deg 14.176 r_long_range_B_refined 7.441 r_long_range_B_other 7.441 r_dihedral_angle_1_deg 5.689 r_angle_other_deg 3.727 r_scangle_other 3.691 r_mcangle_it 2.655 r_mcangle_other 2.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.862 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_3_deg 14.176 r_long_range_B_refined 7.441 r_long_range_B_other 7.441 r_dihedral_angle_1_deg 5.689 r_angle_other_deg 3.727 r_scangle_other 3.691 r_mcangle_it 2.655 r_mcangle_other 2.655 r_scbond_it 2.278 r_scbond_other 2.276 r_angle_refined_deg 1.661 r_mcbond_it 1.6 r_mcbond_other 1.6 r_chiral_restr 0.094 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 5938 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing