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Human glutamate carboxypeptidase II in complex with Antibody- Recruiting Molecule ARM-P2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOT PDB ENTRY 2OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 33% (V/V) PENTAERYTHRITOL PROPOXYLATE PO/OH 5/4, 1% (W/V) PEG 3350, 100 MM TRIS-HCL, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.28 62.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.499 α = 90 b = 130.038 β = 90 c = 158.637 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 MARRESEARCH MX-300 2009-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 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 1.69 30 97.8 0.09 18.4 5.8 114649 -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 1.69 1.75 84.1 0.49 2.1 2.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OOT 1.69 30 112878 1700 97.77 0.15984 0.15947 0.1855 0.18516 0.2083 RANDOM 29.087
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] 1.35 -2.43 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.726 r_dihedral_angle_4_deg 15.011 r_dihedral_angle_3_deg 14.305 r_dihedral_angle_1_deg 5.69 r_scangle_it 5.231 r_scbond_it 3.125 r_mcangle_it 1.869 r_angle_refined_deg 1.847 r_mcbond_it 1.078 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.726 r_dihedral_angle_4_deg 15.011 r_dihedral_angle_3_deg 14.305 r_dihedral_angle_1_deg 5.69 r_scangle_it 5.231 r_scbond_it 3.125 r_mcangle_it 1.869 r_angle_refined_deg 1.847 r_mcbond_it 1.078 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 5525 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing