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Ribose 5-phosphate isomerase from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.4 ul protein 8 mg/ml, 0.4 ul crystallization buffer 200mM NaCl, 0.6 mM KAu(CN)2, 20% PEG 3000,100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.689 α = 90 b = 136.23 β = 90 c = 45.011 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 210 2005-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.03492 ALS 8.2.1
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 2.08 50 92.7 0.073 25.818 5.9 32530
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 2.08 96.6 96.6 0.368 3.916
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UJ5 2.087 50 31605 1571 0.2085 0.2181 0.2716 0.2768 random 25.8
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 38.763 r_dihedral_angle_3_deg 15.02 r_dihedral_angle_4_deg 13.565 r_dihedral_angle_1_deg 7.683 r_scangle_it 4.638 r_scbond_it 3.078 r_mcangle_it 2.227 r_scangle_other 1.912 r_angle_refined_deg 1.625 r_mcbond_it 1.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.763 r_dihedral_angle_3_deg 15.02 r_dihedral_angle_4_deg 13.565 r_dihedral_angle_1_deg 7.683 r_scangle_it 4.638 r_scbond_it 3.078 r_mcangle_it 2.227 r_scangle_other 1.912 r_angle_refined_deg 1.625 r_mcbond_it 1.349 r_mcangle_other 1.027 r_scbond_other 0.918 r_angle_other_deg 0.72 r_mcbond_other 0.27 r_symmetry_vdw_other 0.221 r_xyhbond_nbd_refined 0.218 r_nbd_refined 0.208 r_nbd_other 0.199 r_symmetry_vdw_refined 0.186 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.157 r_nbtor_other 0.095 r_chiral_restr 0.053 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3595 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 10
Software Software Software Name Purpose EPMR phasing PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling REFMAC refinement