☰ Navigation Tabs
Glutamate dehydrogenase-69O
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Potassium phosphate monobasic/Sodium phosphate dibasic buffer (pH 6.2), 10% (w/v) polyethylene glycol (PEG) 3,000, and 10% (v/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.782 α = 90 b = 153.599 β = 115.58 c = 110.55 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS3 6M 2022-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.55 45.04 100 0.166 0.18 0.068 0.995 10.3 6.9 48864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.63 100 1.164 1.259 0.476 0.708 6.9
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 2.55 45.04 46373 2490 99.98 0.21054 0.20796 0.2125 0.26022 0.2623 RANDOM 50.374
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] -1.11 -0.43 -3.39 3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.984 r_long_range_B_refined 8.177 r_long_range_B_other 8.177 r_dihedral_angle_1_deg 6.635 r_scangle_other 6.167 r_dihedral_angle_2_deg 5.747 r_mcangle_it 5.359 r_mcangle_other 5.359 r_scbond_it 3.999 r_scbond_other 3.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.984 r_long_range_B_refined 8.177 r_long_range_B_other 8.177 r_dihedral_angle_1_deg 6.635 r_scangle_other 6.167 r_dihedral_angle_2_deg 5.747 r_mcangle_it 5.359 r_mcangle_other 5.359 r_scbond_it 3.999 r_scbond_other 3.998 r_mcbond_it 3.57 r_mcbond_other 3.569 r_angle_refined_deg 1.321 r_angle_other_deg 0.981 r_chiral_restr 0.061 r_bond_other_d 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 9180 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing