2PVV

Structure of human glutamate carboxypeptidase II (GCPII) in complex with L-serine-O-sulfate


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
3.2962.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.617α = 90
b = 130.22β = 90
c = 158.975γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-12-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.13098.90.09715.44.86030460304-3
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)
12.12.1898.40.5053.74.85928

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 DIFFRACTIONDifference FourierTHROUGHOUT2OOT2.113057236306198.560.176220.174240.21214RANDOM29.73
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]
1.47-2.210.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.892
r_dihedral_angle_4_deg16.406
r_dihedral_angle_3_deg14.712
r_dihedral_angle_1_deg6.431
r_scangle_it4.06
r_scbond_it2.808
r_angle_refined_deg1.803
r_mcangle_it1.769
r_mcbond_it1.127
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.892
r_dihedral_angle_4_deg16.406
r_dihedral_angle_3_deg14.712
r_dihedral_angle_1_deg6.431
r_scangle_it4.06
r_scbond_it2.808
r_angle_refined_deg1.803
r_mcangle_it1.769
r_mcbond_it1.127
r_nbtor_refined0.316
r_symmetry_vdw_refined0.242
r_nbd_refined0.212
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.161
r_chiral_restr0.125
r_metal_ion_refined0.105
r_bond_refined_d0.021
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5529
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms191

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling