2CIJ

membrane-bound glutamate carboxypeptidase II (GCPII) with bound methionine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.25pH 7.25
Crystal Properties
Matthews coefficientSolvent content
3.3563.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.692α = 90
b = 130.777β = 90
c = 160.303γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray260CCDMARRESEARCH2004-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.45099.90.0818.26.342562-337.77
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4999.83.9

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C6G2.45041236133099.90.1740.1720.219RANDOM29.43
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]
1.07-2.11.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.735
r_dihedral_angle_4_deg17.581
r_dihedral_angle_3_deg15.679
r_dihedral_angle_1_deg6.39
r_scangle_it4.065
r_scbond_it2.789
r_angle_refined_deg1.753
r_mcangle_it1.661
r_mcbond_it1.026
r_symmetry_hbond_refined0.379
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.735
r_dihedral_angle_4_deg17.581
r_dihedral_angle_3_deg15.679
r_dihedral_angle_1_deg6.39
r_scangle_it4.065
r_scbond_it2.789
r_angle_refined_deg1.753
r_mcangle_it1.661
r_mcbond_it1.026
r_symmetry_hbond_refined0.379
r_nbtor_refined0.333
r_symmetry_vdw_refined0.315
r_nbd_refined0.239
r_xyhbond_nbd_refined0.183
r_chiral_restr0.129
r_bond_refined_d0.017
r_gen_planes_refined0.007
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_refined
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_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 Atoms5318
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms189

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling