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Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.05M ammonium acetate, 0.1M tris pH 8.0, 16% PEG 10000, 0.05M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.17 α = 108.58 b = 91.23 β = 98.09 c = 102.07 γ = 104.62
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 2018-03-10 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 2.65 93.89 96.5 0.096 0.113 0.06 0.992 9.4 3.6 41560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.76 94.9 0.557 0.657 0.346 0.819 3.6
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 6A34 2.65 93.89 39519 2017 96.41 0.2146 0.2105 0.2164 0.2942 0.2924 RANDOM 57.142
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] -2.34 -0.19 0.14 -0.52 -0.15 2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.57 r_dihedral_angle_3_deg 18.685 r_dihedral_angle_4_deg 14.441 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.52 r_angle_other_deg 0.828 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.57 r_dihedral_angle_3_deg 18.685 r_dihedral_angle_4_deg 14.441 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.52 r_angle_other_deg 0.828 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11168 Nucleic Acid Atoms Solvent Atoms 96 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