2PVW

A high resolution structure of human glutamate carboxypeptidase II (GCPII) in complex with 2-(phosphonomethyl)pentanedioic acid (2-PMPA)


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 3% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3262.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.849α = 90
b = 130.822β = 90
c = 159.452γ = 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
11.713098.60.12615.19.8111281111281-3-3
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)
11.721.7891.70.4953.5610238

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 SYNTHESISTHROUGHOUT2OOT1.7115105604554997.70.182860.181590.20714RANDOM34.647
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]
1.16-2.070.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.443
r_dihedral_angle_3_deg14.141
r_dihedral_angle_4_deg12.807
r_sphericity_free11.398
r_sphericity_bonded7.805
r_dihedral_angle_1_deg5.73
r_scangle_it4.495
r_scbond_it2.969
r_mcangle_it1.907
r_angle_refined_deg1.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.443
r_dihedral_angle_3_deg14.141
r_dihedral_angle_4_deg12.807
r_sphericity_free11.398
r_sphericity_bonded7.805
r_dihedral_angle_1_deg5.73
r_scangle_it4.495
r_scbond_it2.969
r_mcangle_it1.907
r_angle_refined_deg1.808
r_mcbond_it1.254
r_nbtor_refined0.324
r_symmetry_vdw_refined0.223
r_nbd_refined0.211
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.158
r_chiral_restr0.132
r_metal_ion_refined0.066
r_bond_refined_d0.019
r_gen_planes_refined0.009
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
r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5490
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms194

Software

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