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Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SDW pdb entry 3SDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection reagent, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.99 38.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.46 α = 90 b = 84.42 β = 90 c = 96.17 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 2011-06-10 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 1.7 50 94.5 0.044 34.74 9.6 17530 16561 -3 20.011
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 1.7 1.74 80.2 0.256 6.62 5.3 1281
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3SDW 1.7 49.08 16509 832 94.19 0.1438 0.1421 0.1749 0.1263 RANDOM 13.745
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] -0.26 0.68 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.788 r_dihedral_angle_3_deg 10.199 r_dihedral_angle_4_deg 6.074 r_dihedral_angle_1_deg 5.1 r_scangle_it 3.535 r_scbond_it 2.024 r_angle_refined_deg 1.323 r_mcangle_it 1.119 r_mcbond_it 0.641 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.788 r_dihedral_angle_3_deg 10.199 r_dihedral_angle_4_deg 6.074 r_dihedral_angle_1_deg 5.1 r_scangle_it 3.535 r_scbond_it 2.024 r_angle_refined_deg 1.323 r_mcangle_it 1.119 r_mcbond_it 0.641 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction