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GLUTAMATE DEHYDROGENASE (W89F-MUTANT) FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGANDED STATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.8 293 1.6 M lithium sulfate (Wako, Osaka, Japan), 1.7%(w/v) poly-ethylene glycol 8000 (PEG800) (Sigma-Aldrich, St. Louis, USA) and 0.1 M sodium acetate (Wako)
Crystal Properties Matthews coefficient Solvent content 4.04 69.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.355 α = 90 b = 163.248 β = 113.91 c = 132.605 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX SX-165mm 2011-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.028 50 99.8 0.063 18.3 3.788 283125
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.028 2.07 0.293
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.028 21.8 269065 14013 99.58 0.17357 0.17224 0.184 0.19944 0.2089 RANDOM 39.29
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] -1.27 1.54 -1.23 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_4_deg 21.037 r_dihedral_angle_3_deg 16.719 r_long_range_B_refined 9.405 r_long_range_B_other 9.405 r_scangle_other 8.048 r_dihedral_angle_1_deg 6.966 r_scbond_it 5.399 r_scbond_other 5.399 r_mcangle_it 5.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_4_deg 21.037 r_dihedral_angle_3_deg 16.719 r_long_range_B_refined 9.405 r_long_range_B_other 9.405 r_scangle_other 8.048 r_dihedral_angle_1_deg 6.966 r_scbond_it 5.399 r_scbond_other 5.399 r_mcangle_it 5.107 r_mcangle_other 5.107 r_mcbond_it 3.79 r_mcbond_other 3.785 r_angle_refined_deg 1.766 r_angle_other_deg 1.451 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 19378 Nucleic Acid Atoms Solvent Atoms 948 Heterogen Atoms 308
Software Software Software Name Purpose REFMAC refinement