4OC3

X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with CFIBzL, a urea-based inhibitor N~2~-{[(1S)-1-carboxy-2-(furan-2-yl)ethyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.362.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.566α = 90
b = 130.434β = 90
c = 159.017γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.793097.69626696266-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8584.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.7929.52-39463894638142997.310.161350.161350.161040.18108RANDOM29.195
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.957
r_dihedral_angle_4_deg15.822
r_dihedral_angle_3_deg14.563
r_dihedral_angle_1_deg5.864
r_scangle_it4.59
r_scbond_it2.817
r_mcangle_it1.721
r_angle_refined_deg1.705
r_mcbond_it1.012
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.957
r_dihedral_angle_4_deg15.822
r_dihedral_angle_3_deg14.563
r_dihedral_angle_1_deg5.864
r_scangle_it4.59
r_scbond_it2.817
r_mcangle_it1.721
r_angle_refined_deg1.705
r_mcbond_it1.012
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.01
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_mcangle_other
r_scbond_other
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 Atoms5529
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms233

Software

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