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X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with CCIBzL, a urea-based inhibitor N~2~-[(1-carboxycyclopropyl)carbamoyl]-N~6~-(4-iodobenzoyl)-L-lysine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.27 62.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.376 α = 90 b = 129.938 β = 90 c = 158.575 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 CCD MARMOSAIC 300 mm CCD 2009-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 1.85 30 99.9 89273 89273 -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 1.85 1.92 99.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.85 28.47 -3 87605 87605 1319 99.25 0.16101 0.16101 0.16069 0.1615 0.1815 0.1792 RANDOM 36.426
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_4_deg 13.838 r_dihedral_angle_1_deg 5.824 r_scangle_it 4.479 r_scbond_it 2.75 r_mcangle_it 1.669 r_angle_refined_deg 1.646 r_mcbond_it 0.966 r_chiral_restr 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_4_deg 13.838 r_dihedral_angle_1_deg 5.824 r_scangle_it 4.479 r_scbond_it 2.75 r_mcangle_it 1.669 r_angle_refined_deg 1.646 r_mcbond_it 0.966 r_chiral_restr 0.202 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 208
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing