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membrane-bound glutamate carboxypeptidase II (GCPII) in complex with quisqualic acid (quisqualate, alpha-amino-3,5-dioxo-1,2,4- oxadiazolidine-2-propanoic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C6C PDB ENTRY 2C6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20 MM HEPES PH 7.25, 200 MM NACL, 5% (W/V) PEG 400 AND 15% (W/V) PEG 1500.
Crystal Properties Matthews coefficient Solvent content 3.48 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.144 α = 90 b = 130.758 β = 90 c = 159.992 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 260 CCD MARRESEARCH 2004-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.99 50 93.5 0.15 5 20662
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-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C6C 2.99 100 20723 93.2 0.21 0.21 34.08
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] 1.95 -2.6 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.533 r_dihedral_angle_3_deg 20.07 r_dihedral_angle_4_deg 19.129 r_dihedral_angle_1_deg 8.323 r_angle_refined_deg 2.312 r_symmetry_vdw_refined 0.395 r_symmetry_hbond_refined 0.393 r_nbtor_refined 0.355 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.533 r_dihedral_angle_3_deg 20.07 r_dihedral_angle_4_deg 19.129 r_dihedral_angle_1_deg 8.323 r_angle_refined_deg 2.312 r_symmetry_vdw_refined 0.395 r_symmetry_hbond_refined 0.393 r_nbtor_refined 0.355 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.225 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.004 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 5318 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement H data reduction SCALEPACK data scaling REFMAC phasing