3BI1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of methotrexate-Glu


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OOT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3363.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.116α = 90
b = 130.462β = 90
c = 159.456γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

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
11.53099.50.0851910169309169309-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5598.20.622.26.6

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 SYNTHESISTHROUGHOUT2oot1.515166133168399.310.148580.148380.16892RANDOM27.094
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]
0.8-1.650.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.922
r_dihedral_angle_4_deg14.395
r_dihedral_angle_3_deg14.277
r_sphericity_free9.398
r_sphericity_bonded7.639
r_dihedral_angle_1_deg5.64
r_scangle_it5.207
r_scbond_it3.727
r_mcangle_it2.774
r_rigid_bond_restr2.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.922
r_dihedral_angle_4_deg14.395
r_dihedral_angle_3_deg14.277
r_sphericity_free9.398
r_sphericity_bonded7.639
r_dihedral_angle_1_deg5.64
r_scangle_it5.207
r_scbond_it3.727
r_mcangle_it2.774
r_rigid_bond_restr2.258
r_mcbond_it1.961
r_angle_refined_deg1.768
r_nbtor_refined0.325
r_symmetry_hbond_refined0.271
r_symmetry_vdw_refined0.243
r_nbd_refined0.226
r_xyhbond_nbd_refined0.167
r_chiral_restr0.129
r_metal_ion_refined0.065
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5529
Nucleic Acid Atoms
Solvent Atoms710
Heterogen Atoms209

Software

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