4MCP

A high resolution structure of human glutamate carboxypeptidase II (GCPII) in complex with folyl-gamma-L-glutamic acid (pteroyldi-gamma-L-glutamic acid)


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, 0.10 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0960.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.533α = 90
b = 130.176β = 90
c = 158.809γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.654094.50.07722.6119318119318-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7161.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6530117931117931120094.080.150210.150070.16408RANDOM29.545
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]
0.85-2.171.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.593
r_sphericity_free17.809
r_sphericity_bonded15.987
r_dihedral_angle_4_deg15.153
r_dihedral_angle_3_deg14.148
r_dihedral_angle_1_deg5.804
r_rigid_bond_restr3.951
r_scangle_it3.268
r_scbond_it2.045
r_angle_refined_deg1.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.593
r_sphericity_free17.809
r_sphericity_bonded15.987
r_dihedral_angle_4_deg15.153
r_dihedral_angle_3_deg14.148
r_dihedral_angle_1_deg5.804
r_rigid_bond_restr3.951
r_scangle_it3.268
r_scbond_it2.045
r_angle_refined_deg1.488
r_mcangle_it1.283
r_mcbond_it0.735
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5516
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms221

Software

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