3CZD

Crystal structure of human glutaminase in complex with L-glutamate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.4M Lithium sulfate, 100mM Bis-tris-propane pH 7.0, 10mM L-glutamate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
5.3877.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.52α = 90
b = 139.52β = 90
c = 153.95γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMirrors2008-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.97891MAX III911-3

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.430990.0510.04226.99.42965229652
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)RedundancyNumber Unique Reflections (All)
12.42.596.70.2920.2537.48.43276

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2DFW2.429278712787117801000.189820.189820.188540.21RANDOM38.972
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]
-0.83-0.831.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.19
r_dihedral_angle_3_deg15.563
r_dihedral_angle_4_deg15.304
r_dihedral_angle_1_deg6.494
r_scangle_it2.869
r_scbond_it2.002
r_angle_refined_deg1.407
r_mcangle_it1.18
r_mcbond_it0.964
r_angle_other_deg0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.19
r_dihedral_angle_3_deg15.563
r_dihedral_angle_4_deg15.304
r_dihedral_angle_1_deg6.494
r_scangle_it2.869
r_scbond_it2.002
r_angle_refined_deg1.407
r_mcangle_it1.18
r_mcbond_it0.964
r_angle_other_deg0.95
r_xyhbond_nbd_refined0.587
r_nbd_refined0.199
r_symmetry_vdw_refined0.187
r_nbd_other0.182
r_nbtor_refined0.176
r_mcbond_other0.136
r_symmetry_vdw_other0.134
r_nbtor_other0.089
r_chiral_restr0.081
r_symmetry_hbond_refined0.064
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing