4JZ0

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with CTT1055


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5% (w/v) PEG 3350, 100mM Tris-HCl , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3263.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.819α = 90
b = 130.399β = 90
c = 159.987γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.91953APS22-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
11.834091.285814-3-3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT1.8329.5983934171090.880.152610.152220.17097RANDOM38.812
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_deg36.609
r_dihedral_angle_4_deg14.548
r_dihedral_angle_3_deg13.965
r_dihedral_angle_1_deg5.922
r_scangle_it4.501
r_scbond_it2.784
r_angle_refined_deg1.639
r_mcangle_it1.535
r_mcbond_it0.884
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.609
r_dihedral_angle_4_deg14.548
r_dihedral_angle_3_deg13.965
r_dihedral_angle_1_deg5.922
r_scangle_it4.501
r_scbond_it2.784
r_angle_refined_deg1.639
r_mcangle_it1.535
r_mcbond_it0.884
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms5512
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms218

Software

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