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Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.7 M NaCl, 3% PEG 6000, 25% MPD
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.57 α = 90 b = 98.57 β = 90 c = 256.621 γ = 120
Symmetry Space Group P 31 1 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2017-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.35 85.54 100 0.142 0.152 0.054 0.995 11.2 7.8 59895
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 5YFJ 2.35 85.54 56774 3051 100 0.1573 0.1546 0.1652 0.2085 0.2133 RANDOM 32.912
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] 0.53 0.26 0.53 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.964 r_dihedral_angle_4_deg 19.738 r_dihedral_angle_3_deg 17.027 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.84 r_angle_other_deg 1.035 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.964 r_dihedral_angle_4_deg 19.738 r_dihedral_angle_3_deg 17.027 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.84 r_angle_other_deg 1.035 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7638 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction