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Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5 Furan Dicarboxylic and NADH with Intact Polyhistidine Tag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ARZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 100 mM HEPES pH 7, 1.26 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.1 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.439 α = 90 b = 117.545 β = 92.19 c = 131.524 γ = 90
Symmetry Space Group P 1 21 1
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 300 mm CCD 2013-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 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 2.45 50 96.9 0.131 0.131 6.1 3.1 74404
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 2.45 2.49 96.5 0.723 0.798 2.1 3
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 MOLECULAR REPLACEMENT THROUGHOUT 1ARZ 2.45 50 70349 3712 96.86 0.2243 0.2226 0.2264 0.2553 0.2561 RANDOM 49.427
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 -0.28 -2.83 4.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.604 r_dihedral_angle_4_deg 23.099 r_dihedral_angle_3_deg 13.761 r_dihedral_angle_1_deg 6.304 r_angle_other_deg 3.906 r_mcangle_it 2.394 r_angle_refined_deg 1.864 r_mcbond_it 1.408 r_mcbond_other 1.407 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.604 r_dihedral_angle_4_deg 23.099 r_dihedral_angle_3_deg 13.761 r_dihedral_angle_1_deg 6.304 r_angle_other_deg 3.906 r_mcangle_it 2.394 r_angle_refined_deg 1.864 r_mcbond_it 1.408 r_mcbond_other 1.407 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15654 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 535
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing