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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, AMP 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, 20% MPD, 0.1% Low Melting Agarose
Crystal Properties Matthews coefficient Solvent content 3.31 62.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.8 α = 90 b = 98.8 β = 90 c = 256.431 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 2017-03-21 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 2.45 85.56 100 0.109 0.113 0.032 0.999 19.6 12.6 53172
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 2.45 85.56 50474 2618 99.98 0.1704 0.1675 0.1763 0.2253 0.23 RANDOM 41.908
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] 1.22 0.61 1.22 -3.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.258 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 16.614 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.822 r_angle_other_deg 1.021 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.258 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 16.614 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.822 r_angle_other_deg 1.021 r_chiral_restr 0.098 r_bond_refined_d 0.016 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 301 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