2XEG | pdb_00002xeg

Human glutamate carboxypeptidase II in complex with Antibody- Recruiting Molecule ARM-P4


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1833% (V/V) PENTAERYTHRITOL PROPOXYLATE PO/OH 5/4, 1% (W/V) PEG 3350, 100 MM TRIS-HCL, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2962.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.707α = 90
b = 130.039β = 90
c = 159.026γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-BM

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
11.593097.60.0627.87137271-3
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)
11.591.6579.90.525

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OOT1.5930135823137397.590.168790.168580.190.190630.22RANDOM25.815
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]
0.72-1.771.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg14.051
r_dihedral_angle_3_deg13.666
r_dihedral_angle_1_deg5.608
r_scangle_it4.211
r_scbond_it2.582
r_angle_refined_deg1.711
r_mcangle_it1.608
r_mcbond_it0.963
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg14.051
r_dihedral_angle_3_deg13.666
r_dihedral_angle_1_deg5.608
r_scangle_it4.211
r_scbond_it2.582
r_angle_refined_deg1.711
r_mcangle_it1.608
r_mcbond_it0.963
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms5530
Nucleic Acid Atoms
Solvent Atoms612
Heterogen Atoms232

Software

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