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Crystal structure of a putative ribose-5-phosphate isomerase from Coccidioides immitis solved by combined iodide ion SAD and MR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 CoimA.00584.a.A1 PS00647 82 mg/mL against JCSG+ screen condition B9, 20% PEG 6000, 0.1 M Na Citrate pH 5.0, and soaked into 20% PEG 6000, 0.1 M Na Citrate pH 5.0, 0.7 M NaI, 22% ethylene glycol for one minute, crystal tracking ID 216516b9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.15 α = 90 b = 49.89 β = 108.62 c = 61.97 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+ 2011-01-11 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 1.9 50 98.9 0.055 20.49 5.8 23781 23513 -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 1.9 1.95 87.5 0.152 6 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD, MOLECULAR REPLACEMENT THROUGHOUT 1.9 50 22275 1205 98.87 0.16637 0.16423 0.1665 0.20508 0.2059 RANDOM 18.317
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] 1.11 -0.08 -0.39 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.448 r_dihedral_angle_4_deg 13.156 r_dihedral_angle_3_deg 12.031 r_dihedral_angle_1_deg 7.517 r_scangle_it 3.778 r_scbond_it 2.329 r_angle_refined_deg 1.364 r_mcangle_it 1.313 r_mcbond_it 0.729 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.448 r_dihedral_angle_4_deg 13.156 r_dihedral_angle_3_deg 12.031 r_dihedral_angle_1_deg 7.517 r_scangle_it 3.778 r_scbond_it 2.329 r_angle_refined_deg 1.364 r_mcangle_it 1.313 r_mcbond_it 0.729 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 2369 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 37
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction