6ETY

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor JHU3371


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BI1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.362.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.646α = 90
b = 130.72β = 90
c = 158.234γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9796PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.683098.90.0620.0690.99914.725.13118798
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7896.10.6930.7750.8842.084.95

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 SYNTHESISTHROUGHOUT3BI11.6830115124357399.260.155570.154870.1777RANDOM32.915
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]
0.5-1.971.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.573
r_dihedral_angle_4_deg15.562
r_dihedral_angle_3_deg13.866
r_long_range_B_refined6.064
r_dihedral_angle_1_deg5.954
r_scbond_it2.097
r_mcangle_it1.871
r_angle_refined_deg1.637
r_mcbond_it1.188
r_chiral_restr0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.573
r_dihedral_angle_4_deg15.562
r_dihedral_angle_3_deg13.866
r_long_range_B_refined6.064
r_dihedral_angle_1_deg5.954
r_scbond_it2.097
r_mcangle_it1.871
r_angle_refined_deg1.637
r_mcbond_it1.188
r_chiral_restr0.118
r_bond_refined_d0.015
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms5546
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms223

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building