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Crystal structure of Geodermatophilus obscurus L-ribose isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 1.26M (NH4)2SO4, Tris, Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.533 α = 90 b = 123.226 β = 97.38 c = 109.446 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS VII 2014-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.9 27.06 91.8 0.266 5 3.2 26574 143.3
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 2.9 2.95 73 0.446 1.31 1.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WW3 2.9 27.06 24303 2397 91.9 0.246 0.246 0.2463 0.294 0.2935 RANDOM 27.7
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] -4.81 -1.8 -3.58 8.39
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.3 c_scangle_it 3.15 c_mcangle_it 2.49 c_scbond_it 2.01 c_mcbond_it 1.66 c_angle_deg 1.5 c_improper_angle_d 1.18 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.3 c_scangle_it 3.15 c_mcangle_it 2.49 c_scbond_it 2.01 c_mcbond_it 1.66 c_angle_deg 1.5 c_improper_angle_d 1.18 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7572 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose CNS refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing