4MCS

A high resolution structure of human glutamate carboxypeptidase II (GCPII) His475Tyr variant in complex with glutamic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5% (w/v) PEG 3350, 0.10 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0960.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.547α = 90
b = 130.395β = 90
c = 158.98γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252010-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

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
11.833093.30.06716.58681686816-3-3
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)
11.831.988.30.4292.12.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8328.538487184871173692.970.159240.158580.19058RANDOM31.482
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.528
r_dihedral_angle_4_deg17.94
r_dihedral_angle_3_deg14.574
r_dihedral_angle_1_deg6.029
r_scangle_it3.877
r_scbond_it2.469
r_angle_refined_deg1.605
r_mcangle_it1.409
r_mcbond_it0.855
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.528
r_dihedral_angle_4_deg17.94
r_dihedral_angle_3_deg14.574
r_dihedral_angle_1_deg6.029
r_scangle_it3.877
r_scbond_it2.469
r_angle_refined_deg1.605
r_mcangle_it1.409
r_mcbond_it0.855
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms5501
Nucleic Acid Atoms
Solvent Atoms584
Heterogen Atoms199

Software

Software
Software NamePurpose
BL-Controldata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing