2C6C

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with GPI-18431 (S)-2-(4-iodobenzylphosphonomethyl)-pentanedioic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.2520 MM HEPES PH 7.25, 200 MM NACL, 5% (W/V) PEG 400 AND 15% (W/V) PEG 1500.
Crystal Properties
Matthews coefficientSolvent content
3.4163.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.127α = 90
b = 131.189β = 90
c = 161.225γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray261CCDMARRESEARCH2002-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.9537, 1.26EMBL/DESY, HAMBURGBW7A

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
124094.30.0715.84.869874-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0796.7

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 DIFFRACTIONSADTHROUGHOUT22568848102494.20.1910.190.225RANDOM32.26
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]
0.99-2.411.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.376
r_scangle_it3.092
r_mcangle_it2.754
r_scbond_it1.947
r_angle_refined_deg1.832
r_mcbond_it1.797
r_angle_other_deg0.869
r_symmetry_vdw_refined0.388
r_symmetry_vdw_other0.3
r_symmetry_hbond_refined0.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.376
r_scangle_it3.092
r_mcangle_it2.754
r_scbond_it1.947
r_angle_refined_deg1.832
r_mcbond_it1.797
r_angle_other_deg0.869
r_symmetry_vdw_refined0.388
r_symmetry_vdw_other0.3
r_symmetry_hbond_refined0.261
r_nbd_other0.258
r_nbd_refined0.231
r_xyhbond_nbd_refined0.21
r_chiral_restr0.12
r_nbtor_other0.096
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_gen_planes_other0.01
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5330
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms187

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing