6HKZ

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-49-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4 2 % (w/v) PEG 3350 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthew coefficientSolvent content
3.4564.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.956α = 90
b = 132.259β = 90
c = 161.589γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS PILATUS 6M2017-08-23MSINGLE 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
12.095099.20.09112.564.564380
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)
12.092.2197.40.6662.054.6

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 SYNTHESISTHROUGHOUT3BI12.0947.5963218210099.250.171480.170430.20308RANDOM57.595
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]
1.86-3.671.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.391
r_dihedral_angle_4_deg16.85
r_dihedral_angle_3_deg15.205
r_dihedral_angle_1_deg6.571
r_long_range_B_other6.168
r_long_range_B_refined6.168
r_scangle_other5.155
r_mcangle_it3.626
r_mcangle_other3.626
r_scbond_it3.574
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.391
r_dihedral_angle_4_deg16.85
r_dihedral_angle_3_deg15.205
r_dihedral_angle_1_deg6.571
r_long_range_B_other6.168
r_long_range_B_refined6.168
r_scangle_other5.155
r_mcangle_it3.626
r_mcangle_other3.626
r_scbond_it3.574
r_scbond_other3.573
r_mcbond_it2.762
r_mcbond_other2.761
r_angle_refined_deg1.656
r_angle_other_deg0.67
r_chiral_restr0.074
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5529
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms211

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing