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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 AMP
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, 0.1% Low Melting Agarose
Crystal Properties Matthews coefficient Solvent content 3.25 62.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.14 α = 90 b = 98.14 β = 90 c = 255.681 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 2016-12-03 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 2.75 85.23 100 0.154 0.165 0.058 0.995 12 7.9 37157
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 2.75 85.23 35206 1890 100 0.1555 0.1519 0.1635 0.224 0.2221 RANDOM 36.164
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] 0.99 0.5 0.99 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.681 r_dihedral_angle_4_deg 20.761 r_dihedral_angle_3_deg 17.757 r_dihedral_angle_1_deg 6.489 r_angle_refined_deg 1.744 r_angle_other_deg 1.004 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.681 r_dihedral_angle_4_deg 20.761 r_dihedral_angle_3_deg 17.757 r_dihedral_angle_1_deg 6.489 r_angle_refined_deg 1.744 r_angle_other_deg 1.004 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 254 Heterogen Atoms 134
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data processing Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction