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Human glutamate carboxypeptidase II in complex with Antibody- Recruiting Molecule ARM-P4
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 3.29 62.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.707 α = 90 b = 130.039 β = 90 c = 159.026 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 2009-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 1.59 30 97.6 0.06 27.8 7 137271 -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 1.59 1.65 79.9 0.5 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 1.59 30 135823 1373 97.59 0.16879 0.16858 0.1947 0.19063 0.2157 RANDOM 25.815
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] 0.72 -1.77 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 14.051 r_dihedral_angle_3_deg 13.666 r_dihedral_angle_1_deg 5.608 r_scangle_it 4.211 r_scbond_it 2.582 r_angle_refined_deg 1.711 r_mcangle_it 1.608 r_mcbond_it 0.963 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 14.051 r_dihedral_angle_3_deg 13.666 r_dihedral_angle_1_deg 5.608 r_scangle_it 4.211 r_scbond_it 2.582 r_angle_refined_deg 1.711 r_mcangle_it 1.608 r_mcbond_it 0.963 r_chiral_restr 0.126 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_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 5530 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing