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Crystal structure of Ribose-5-phosphate isomerase A from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KS2 pdb entry 1KS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Internal tracking number 225985D11. WIZARD 3/4 screen condition D11: 30%(w/v) PEG 5000 MME, 0.1M MES 6.5, 0.2M Ammonium sulfate. ButhA.00944.a.A1 PW33411 at 33.6 mg/ml. , VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.09 α = 90 b = 73.47 β = 128.05 c = 52.01 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 CCD RIGAKU SATURN 944+ 2011-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 2.1 50 94.8 0.046 21.23 3.7 15098 -3 19.877
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 2.1 2.15 78.9 0.092 12.9 3.3
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 pdb entry 1KS2 2.1 47.86 15098 804 98.86 0.162 0.16 0.1677 0.207 0.2036 RANDOM 15.244
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] -0.61 -0.12 0.28 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.449 r_dihedral_angle_4_deg 15.436 r_dihedral_angle_3_deg 11.537 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.462 r_angle_other_deg 0.888 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.449 r_dihedral_angle_4_deg 15.436 r_dihedral_angle_3_deg 11.537 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.462 r_angle_other_deg 0.888 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction