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X-ray structure of human glutamate carboxypeptidase II (the E424A inactive mutant) in complex with N-acetyl-aspartyl-methionine
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 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.539 α = 90 b = 129.937 β = 90 c = 159.194 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 2006-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.66 30 99.9 0.62 27.6 8.2 120007 120007 -3 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.66 28.21 120007 1815 98.27 0.18026 0.1799 0.1902 0.20449 0.2115 RANDOM 30.898
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 35.428 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_1_deg 6.458 r_scangle_it 3.832 r_scbond_it 2.425 r_angle_refined_deg 1.688 r_mcangle_it 1.614 r_mcbond_it 0.957 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_1_deg 6.458 r_scangle_it 3.832 r_scbond_it 2.425 r_angle_refined_deg 1.688 r_mcangle_it 1.614 r_mcbond_it 0.957 r_chiral_restr 0.121 r_bond_refined_d 0.018 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5489 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 172
Software Software Software Name Purpose SERGUI data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing