5ELY

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU242


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828833% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2962.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.06α = 90
b = 130.827β = 90
c = 158.386γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252011-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.81100.8799.4825.42695135
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.87

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 SYNTHESISTHROUGHOUT1.81409401395299.50.17770.17750.1986RANDOM32.89
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]
1.18-2.020.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.169
r_dihedral_angle_4_deg15.023
r_dihedral_angle_3_deg14.65
r_dihedral_angle_1_deg6.207
r_scangle_it4.102
r_scbond_it2.577
r_mcangle_it1.683
r_angle_refined_deg1.658
r_mcbond_it1.014
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.169
r_dihedral_angle_4_deg15.023
r_dihedral_angle_3_deg14.65
r_dihedral_angle_1_deg6.207
r_scangle_it4.102
r_scbond_it2.577
r_mcangle_it1.683
r_angle_refined_deg1.658
r_mcbond_it1.014
r_chiral_restr0.13
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5436
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MxCuBEdata collection