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Crystal structure of ligand-free form of 5-ketofructose reductase of Gluconobacter sp. strain CHM43
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 PEG3350, HEPES-Na, calcium acetate, ethylene glycol, 1,4-butanediol
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.527 α = 90 b = 63.475 β = 93.42 c = 93.919 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 PIXEL DECTRIS EIGER X 4M 2016-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.100 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.5 93.751 99.5 0.094 0.107 0.05 9.4 4.5 77600 77600
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 99.8 0.51 0.51 0.577 0.266 1.1 4.7
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 1NVT 1.5 41.45 73708 3862 99.37 0.2331 0.2319 0.2319 0.2544 0.2542 RANDOM 17.951
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] 0.02 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.788 r_dihedral_angle_4_deg 16.504 r_dihedral_angle_3_deg 14.414 r_dihedral_angle_1_deg 5.364 r_angle_refined_deg 1.387 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3992 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing