2JBK

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with quisqualic acid (quisqualate, alpha-amino-3,5-dioxo-1,2,4- oxadiazolidine-2-propanoic acid)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C6CPDB ENTRY 2C6C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720 MM HEPES PH 7.25, 200 MM NACL, 5% (W/V) PEG 400 AND 15% (W/V) PEG 1500.
Crystal Properties
Matthews coefficientSolvent content
3.4864.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.144α = 90
b = 130.758β = 90
c = 159.992γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray260CCDMARRESEARCH2004-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.995093.50.15520662

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C6C2.991002072393.20.210.2134.08
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]
1.95-2.60.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.533
r_dihedral_angle_3_deg20.07
r_dihedral_angle_4_deg19.129
r_dihedral_angle_1_deg8.323
r_angle_refined_deg2.312
r_symmetry_vdw_refined0.395
r_symmetry_hbond_refined0.393
r_nbtor_refined0.355
r_nbd_refined0.295
r_xyhbond_nbd_refined0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.533
r_dihedral_angle_3_deg20.07
r_dihedral_angle_4_deg19.129
r_dihedral_angle_1_deg8.323
r_angle_refined_deg2.312
r_symmetry_vdw_refined0.395
r_symmetry_hbond_refined0.393
r_nbtor_refined0.355
r_nbd_refined0.295
r_xyhbond_nbd_refined0.225
r_chiral_restr0.143
r_bond_refined_d0.024
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 AtomsNumber
Protein Atoms5318
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms193

Software

Software
Software NamePurpose
REFMACrefinement
Hdata reduction
SCALEPACKdata scaling
REFMACphasing