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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 1Q0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M Sodium citrate/citric acid pH 5.0
1.2 M Ammonium phosphate dibasic
0.2 M Sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.533 α = 90 b = 148.923 β = 90 c = 244.055 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 2013-03-07 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 2.35 50 99.9 0.05 0.05 33.2 4.5 49916 -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 2.35 2.39 100 0.275 0.948 4.7 4.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1Q0L 2.35 50 47370 2455 99.61 0.18605 0.18478 0.21014 0.2091 RANDOM 57.276
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] 5.95 -3.37 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.303 r_dihedral_angle_4_deg 16.785 r_dihedral_angle_3_deg 13.891 r_long_range_B_refined 7.05 r_long_range_B_other 7.05 r_dihedral_angle_1_deg 5.616 r_scangle_other 4.909 r_mcangle_it 3.411 r_mcangle_other 3.411 r_scbond_it 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.303 r_dihedral_angle_4_deg 16.785 r_dihedral_angle_3_deg 13.891 r_long_range_B_refined 7.05 r_long_range_B_other 7.05 r_dihedral_angle_1_deg 5.616 r_scangle_other 4.909 r_mcangle_it 3.411 r_mcangle_other 3.411 r_scbond_it 2.97 r_scbond_other 2.968 r_mcbond_it 2.115 r_mcbond_other 2.112 r_angle_refined_deg 1.639 r_angle_other_deg 1.243 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.004 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 5960 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-3000 phasing HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing