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Crystal structure of Glutamate dehydrogenase from Peptoniphilus asaccharolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1 M SODIUM CACODYLATE PH 6.5, 200 MM NACL
Crystal Properties Matthews coefficient Solvent content 3.82 67.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.314 α = 90 b = 153.314 β = 90 c = 318.993 γ = 120
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 MARMOSAIC 225 mm CCD 2009-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.94 50 99.8 0.12 18.7 11.5 58934 -3 72.9
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 2.94 3.01 97.8 0.59 2.9 8.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 2.94 20 29106 1015 97.78 0.24389 0.24235 0.28693 0.2963 RANDOM 79.616
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] -0.41 0.21 -0.41 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.422 r_dihedral_angle_4_deg 19.773 r_dihedral_angle_3_deg 18.666 r_dihedral_angle_1_deg 6.94 r_scangle_it 2.274 r_angle_refined_deg 1.439 r_scbond_it 1.42 r_mcangle_it 0.755 r_mcbond_it 0.443 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.422 r_dihedral_angle_4_deg 19.773 r_dihedral_angle_3_deg 18.666 r_dihedral_angle_1_deg 6.94 r_scangle_it 2.274 r_angle_refined_deg 1.439 r_scbond_it 1.42 r_mcangle_it 0.755 r_mcbond_it 0.443 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6082 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling Auto-Rickshaw phasing