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Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N 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, 20% MPD
Crystal Properties Matthews coefficient Solvent content 2.61 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.13 α = 90 b = 81.13 β = 90 c = 100.18 γ = 120
Symmetry Space Group P 3 2 1
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 2016-11-23 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 2.7 100.18 100 0.09 0.094 0.029 0.998 23 10.3 10900
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 2.7 100.18 10348 552 99.99 0.1809 0.1765 0.1831 0.2644 0.2579 RANDOM 48.382
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] -1.85 -0.93 -1.85 6.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.624 r_dihedral_angle_4_deg 21.581 r_dihedral_angle_3_deg 17.002 r_dihedral_angle_1_deg 6.875 r_angle_refined_deg 1.651 r_angle_other_deg 0.961 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.624 r_dihedral_angle_4_deg 21.581 r_dihedral_angle_3_deg 17.002 r_dihedral_angle_1_deg 6.875 r_angle_refined_deg 1.651 r_angle_other_deg 0.961 r_chiral_restr 0.085 r_bond_refined_d 0.011 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 2538 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 41
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