3FEE

The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with quisqualic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FEDPDB entry 3FED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES-Na, 10% (w/v) PEG6000, 5% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9458.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.985α = 90
b = 103.69β = 108.27
c = 77.611γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2006-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.2759APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.565099.20.0493.6130199130199-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.62970.2614.93.512705

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3FED1.5625128862131399.30.149660.149330.18438RANDOM17.561
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]
0.120.21-0.120.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.021
r_dihedral_angle_4_deg18.757
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg5.846
r_scangle_it4.042
r_scbond_it2.532
r_angle_refined_deg1.858
r_mcangle_it1.664
r_mcbond_it1.002
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.021
r_dihedral_angle_4_deg18.757
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg5.846
r_scangle_it4.042
r_scbond_it2.532
r_angle_refined_deg1.858
r_mcangle_it1.664
r_mcbond_it1.002
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5496
Nucleic Acid Atoms
Solvent Atoms828
Heterogen Atoms87

Software

Software
Software NamePurpose
MAR345dtbdata collection
XFITdata reduction
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling