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Crystal structure of human glutaminase in complex with L-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFW PDB entry 2DFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.4M Lithium sulfate, 100mM Bis-tris-propane pH 7.0, 10mM L-glutamate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.38 77.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.52 α = 90 b = 139.52 β = 90 c = 153.95 γ = 90
Symmetry Space Group I 41 2 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 CCD MARMOSAIC 225 mm CCD Mirrors 2008-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.97891 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 30 99 0.051 0.042 26.9 9.4 29652 29652
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 96.7 0.292 0.253 7.4 8.4 3276
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2DFW 2.4 29 27871 27871 1780 100 0.18982 0.18982 0.18854 0.21 0.2285 RANDOM 38.972
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] -0.83 -0.83 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.19 r_dihedral_angle_3_deg 15.563 r_dihedral_angle_4_deg 15.304 r_dihedral_angle_1_deg 6.494 r_scangle_it 2.869 r_scbond_it 2.002 r_angle_refined_deg 1.407 r_mcangle_it 1.18 r_mcbond_it 0.964 r_angle_other_deg 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.19 r_dihedral_angle_3_deg 15.563 r_dihedral_angle_4_deg 15.304 r_dihedral_angle_1_deg 6.494 r_scangle_it 2.869 r_scbond_it 2.002 r_angle_refined_deg 1.407 r_mcangle_it 1.18 r_mcbond_it 0.964 r_angle_other_deg 0.95 r_xyhbond_nbd_refined 0.587 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.187 r_nbd_other 0.182 r_nbtor_refined 0.176 r_mcbond_other 0.136 r_symmetry_vdw_other 0.134 r_nbtor_other 0.089 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.064 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing