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Crystal structure of a ribose-5-phosphate isomerase B RpiB from Coccidioides immitis bound to phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QD5 PDB ENTRY 3qd5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 CoimA.00584.a.A1 PS00647 at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2 against PACT screen condition A2 0.1 M SPG buffer pH 5.0, 25% PEG 1500 with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID 222975a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.7 α = 90 b = 85.22 β = 90 c = 96.29 γ = 90
Symmetry Space Group F 2 2 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 RIGAKU SATURN 944+ VariMax 2011-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 1.8 50 99.8 0.119 12.3 3.6 28652 -3 19.61
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 1.8 1.85 98.8 0.438 2.08 2 2133
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 3qd5 1.8 30.24 14922 752 99.47 0.15 0.1486 0.1585 0.1762 0.1726 RANDOM 13.1584
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] -0.28 0.72 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.981 r_dihedral_angle_4_deg 11.876 r_dihedral_angle_3_deg 10.645 r_dihedral_angle_1_deg 5.142 r_scangle_it 3.313 r_scbond_it 1.996 r_angle_refined_deg 1.288 r_mcangle_it 1.069 r_mcbond_it 0.633 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.981 r_dihedral_angle_4_deg 11.876 r_dihedral_angle_3_deg 10.645 r_dihedral_angle_1_deg 5.142 r_scangle_it 3.313 r_scbond_it 1.996 r_angle_refined_deg 1.288 r_mcangle_it 1.069 r_mcbond_it 0.633 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1179 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 14
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction