☰ Navigation Tabs
X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of methotrexate-Glu
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOT
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 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.116 α = 90 b = 130.462 β = 90 c = 159.456 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 2006-07-24 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 1.5 30 99.5 0.085 19 10 169309 169309 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 98.2 0.62 2.2 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2oot 1.5 15 166133 1683 99.31 0.14858 0.14838 0.1521 0.16892 0.1721 RANDOM 27.094
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] 0.8 -1.65 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.922 r_dihedral_angle_4_deg 14.395 r_dihedral_angle_3_deg 14.277 r_sphericity_free 9.398 r_sphericity_bonded 7.639 r_dihedral_angle_1_deg 5.64 r_scangle_it 5.207 r_scbond_it 3.727 r_mcangle_it 2.774 r_rigid_bond_restr 2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.922 r_dihedral_angle_4_deg 14.395 r_dihedral_angle_3_deg 14.277 r_sphericity_free 9.398 r_sphericity_bonded 7.639 r_dihedral_angle_1_deg 5.64 r_scangle_it 5.207 r_scbond_it 3.727 r_mcangle_it 2.774 r_rigid_bond_restr 2.258 r_mcbond_it 1.961 r_angle_refined_deg 1.768 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.271 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.129 r_metal_ion_refined 0.065 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling