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X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with COIBzL, a urea-based inhibitor (2S)-2-[({(1S)-1-carboxy-2-[(2S)-oxiran-2-yl]ethyl}carbamoyl)amino]-6-[(4-iodobenzoyl)amino]hexanoic acid
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 3.29 62.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.396 α = 90 b = 130.353 β = 90 c = 158.944 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 225 mm CCD 2009-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
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 1.75 30 99.8 105692 105692 -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 1.75 1.81 99
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 1.75 29.48 -3 104328 104328 1053 99.58 0.16832 0.16832 0.16807 0.1678 0.19294 0.1948 RANDOM 28.685
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] -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.525 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_1_deg 5.855 r_scangle_it 4.558 r_scbond_it 2.802 r_mcangle_it 1.731 r_angle_refined_deg 1.722 r_mcbond_it 0.992 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.525 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_1_deg 5.855 r_scangle_it 4.558 r_scbond_it 2.802 r_mcangle_it 1.731 r_angle_refined_deg 1.722 r_mcbond_it 0.992 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5528 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 210
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing