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Crystal Structure of the Catalytic Domain of Inosine Monophosphate Dehydrogenase (IMPDH) from Methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CU0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 297 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 30% v/v polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.65 α = 90 b = 97.65 β = 90 c = 168.22 γ = 90
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 MAR scanner 345 mm plate 2018-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 53.37 100 0.845 4 4.4 24178
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 0.845
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 2cu0 2.6 53.37 22945 1233 99.98 0.25525 0.25416 0.2624 0.27606 0.2777 RANDOM 15.675
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] -0.6 -0.6 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.029 r_dihedral_angle_3_deg 18.403 r_dihedral_angle_4_deg 14.228 r_dihedral_angle_1_deg 8.059 r_long_range_B_refined 3.173 r_long_range_B_other 3.165 r_angle_refined_deg 1.559 r_angle_other_deg 1.365 r_mcangle_it 1.336 r_mcangle_other 1.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.029 r_dihedral_angle_3_deg 18.403 r_dihedral_angle_4_deg 14.228 r_dihedral_angle_1_deg 8.059 r_long_range_B_refined 3.173 r_long_range_B_other 3.165 r_angle_refined_deg 1.559 r_angle_other_deg 1.365 r_mcangle_it 1.336 r_mcangle_other 1.336 r_scangle_other 1.099 r_mcbond_it 0.762 r_mcbond_other 0.762 r_scbond_it 0.614 r_scbond_other 0.613 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4756 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing