3FED

The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with a transition state analog of Glu-Glu


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OR4PDB entry 2OR4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES-Na, 10% (w/v) PEG6000, 5% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9558.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.731α = 90
b = 104.086β = 108.19
c = 77.634γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-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
11.293097.80.0926.6227958227958-3-3
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)
11.291.3479.80.4691.9318560

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2OR41.2925225644229298.740.131040.130870.14727RANDOM18.382
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]
0.030.250.35-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.741
r_dihedral_angle_4_deg18.777
r_dihedral_angle_3_deg13.484
r_sphericity_free9.96
r_dihedral_angle_1_deg5.86
r_sphericity_bonded5.474
r_scangle_it5.186
r_scbond_it3.568
r_mcangle_it2.701
r_rigid_bond_restr2.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.741
r_dihedral_angle_4_deg18.777
r_dihedral_angle_3_deg13.484
r_sphericity_free9.96
r_dihedral_angle_1_deg5.86
r_sphericity_bonded5.474
r_scangle_it5.186
r_scbond_it3.568
r_mcangle_it2.701
r_rigid_bond_restr2.058
r_mcbond_it1.862
r_angle_refined_deg1.83
r_chiral_restr0.125
r_bond_refined_d0.017
r_gen_planes_refined0.014
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5504
Nucleic Acid Atoms
Solvent Atoms861
Heterogen Atoms94

Software

Software
Software NamePurpose
MAR345dtbdata collection
Cootmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling