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Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VM6
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 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.63 α = 90 b = 98.63 β = 90 c = 257.061 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 2016-10-31 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 2.2 85.69 99.5 0.092 0.098 0.031 0.998 17.8 9.9 72651
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 3VM6 2.2 85.69 68993 3615 99.4 0.1517 0.1497 0.1581 0.1897 0.1925 RANDOM 36.644
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] 0.43 0.21 0.43 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.125 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 16.084 r_dihedral_angle_1_deg 6.078 r_angle_refined_deg 1.903 r_angle_other_deg 1.046 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.125 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 16.084 r_dihedral_angle_1_deg 6.078 r_angle_refined_deg 1.903 r_angle_other_deg 1.046 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 507 Heterogen Atoms 82
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