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Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ribulose 3-Epimerase with Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100mM MES, 5%(w/v) PEG1000, 20%(v/v) PEG200
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.318 α = 107.22 b = 55.275 β = 102.71 c = 58.699 γ = 91.75
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 ADSC QUANTUM 315r 2014-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97960 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.4 50 94.5 0.05 25.79 3.9 98787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 93.8 0.323 4.04 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZVR 1.446 21.581 1.98 96613 4833 92.14 0.1752 0.174 0.1737 0.1993 0.1982
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.952 f_angle_d 0.855 f_chiral_restr 0.075 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4258 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing MOLREP phasing Coot model building