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X-ray structure of human glutamate carboxypeptidase II in complex with DCCBL, a urea based inhibitor with distal carborane moiety
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5 % (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.316 α = 90 b = 130.564 β = 90 c = 158.073 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.0 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.79 50 99.3 97220 97220 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.9 96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.79 28.43 92337 92336 4859 99.33 0.15875 0.15744 0.18404 0.1808 RANDOM 25.962
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] -0.15 0.4 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.609 r_dihedral_angle_4_deg 14.869 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 5.991 r_scbond_it 1.982 r_mcangle_it 1.796 r_angle_refined_deg 1.576 r_mcbond_it 1.152 r_chiral_restr 0.114 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.609 r_dihedral_angle_4_deg 14.869 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 5.991 r_scbond_it 1.982 r_mcangle_it 1.796 r_angle_refined_deg 1.576 r_mcbond_it 1.152 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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_it 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 Atoms Number Protein Atoms 5512 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 227
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing