6H7Z

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-65-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BI1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829334% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2862.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.222α = 90
b = 130.389β = 90
c = 158.469γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2017-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.34

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
1230.81000.17611.913.270883
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)
122.041000.8842.311.5

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3BI123067160358999.750.172010.170190.20594RANDOM23.254
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]
0.67-1.320.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.304
r_dihedral_angle_4_deg17.09
r_dihedral_angle_3_deg15.75
r_dihedral_angle_1_deg6.635
r_long_range_B_refined6.294
r_long_range_B_other6.294
r_scangle_other2.643
r_angle_refined_deg1.79
r_mcangle_it1.761
r_mcangle_other1.761
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.304
r_dihedral_angle_4_deg17.09
r_dihedral_angle_3_deg15.75
r_dihedral_angle_1_deg6.635
r_long_range_B_refined6.294
r_long_range_B_other6.294
r_scangle_other2.643
r_angle_refined_deg1.79
r_mcangle_it1.761
r_mcangle_other1.761
r_scbond_it1.586
r_scbond_other1.586
r_mcbond_it1.052
r_mcbond_other1.052
r_angle_other_deg0.708
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5538
Nucleic Acid Atoms
Solvent Atoms546
Heterogen Atoms314

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
REFMACphasing
Cootmodel building