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Structure of mutant of ribose 5-phosphate isomerase type B from Trypanosoma cruzi.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NN4 pdb entry 1NN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 0.8 M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.079 α = 90 b = 93.079 β = 90 c = 93.827 γ = 90
Symmetry Space Group P 42 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 2008-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.4 30 98.2 0.097 0.097 11.1 5.7 79637
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 100 0.335 0.335 3.1 5.7 11693
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 (All) 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 1NN4 1.4 30 79570 3977 97.78 0.223 0.223 0.223 0.2223 0.232 0.233 RANDOM 16.949
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.721 r_dihedral_angle_4_deg 16.608 r_dihedral_angle_3_deg 11.612 r_dihedral_angle_1_deg 4.304 r_scangle_it 1.943 r_scbond_it 1.2 r_angle_refined_deg 0.943 r_mcangle_it 0.823 r_mcbond_it 0.488 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.721 r_dihedral_angle_4_deg 16.608 r_dihedral_angle_3_deg 11.612 r_dihedral_angle_1_deg 4.304 r_scangle_it 1.943 r_scbond_it 1.2 r_angle_refined_deg 0.943 r_mcangle_it 0.823 r_mcbond_it 0.488 r_nbtor_refined 0.299 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.083 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection SCALA data scaling