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Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archeal and bacterial enzymes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LK5 pdb entry 1LK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M Magnesium Chloride, 30% Polyethylene Glycol 4000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.4 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.24 α = 90 b = 209.24 β = 90 c = 209.24 γ = 90
Symmetry Space Group F 4 3 2
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 MARRESEARCH 2004-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 0.134 19 5.1 23476
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.25 100 0.63 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 1LK5 2.1 10 23182 22023 1159 100 0.19529 0.1926 0.1922 0.24733 0.2467 RANDOM 30.368
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 r_dihedral_angle_2_deg 39.851 r_dihedral_angle_4_deg 28.178 r_dihedral_angle_3_deg 15.497 r_dihedral_angle_1_deg 6.572 r_scangle_it 4.196 r_scbond_it 2.843 r_mcangle_it 1.86 r_angle_refined_deg 1.59 r_mcbond_it 1.143 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.851 r_dihedral_angle_4_deg 28.178 r_dihedral_angle_3_deg 15.497 r_dihedral_angle_1_deg 6.572 r_scangle_it 4.196 r_scbond_it 2.843 r_mcangle_it 1.86 r_angle_refined_deg 1.59 r_mcbond_it 1.143 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.268 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1930 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling BEAST phasing