5OF0

X-ray structure of human glutamate carboxypeptidase II (GCPII), the E424M inactive mutant, in complex with a inhibitor CFBzOG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthew coefficientSolvent content
3.3262.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.467α = 90
b = 130.461β = 90
c = 159.574γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.4849.2598.90.040.018117.65.2173724
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.593.90.6730.3140.8491.95.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3BI11.4849.25170339338298.780.157080.156780.17197RANDOM38.483
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]
0.9-2.371.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.459
r_dihedral_angle_4_deg14.364
r_dihedral_angle_3_deg13.779
r_dihedral_angle_1_deg5.884
r_long_range_B_refined4.567
r_long_range_B_other4.435
r_scangle_other3.295
r_scbond_it2.13
r_scbond_other2.13
r_mcangle_other2.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.459
r_dihedral_angle_4_deg14.364
r_dihedral_angle_3_deg13.779
r_dihedral_angle_1_deg5.884
r_long_range_B_refined4.567
r_long_range_B_other4.435
r_scangle_other3.295
r_scbond_it2.13
r_scbond_other2.13
r_mcangle_other2.041
r_mcangle_it2.04
r_angle_other_deg1.714
r_angle_refined_deg1.691
r_mcbond_it1.389
r_mcbond_other1.386
r_chiral_restr0.116
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5512
Nucleic Acid Atoms
Solvent Atoms614
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
REFMACphasing
Cootmodel building
XDSdata reduction