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Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y0L PDB ENTRY 1Y0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.7 33% PEG 2000, 0.2M CDCL2, 0.1M BIS- TRIS-PROPANE, PH 6.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 6.70
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.069 α = 89.89 b = 106.299 β = 90.04 c = 116.109 γ = 89.48
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 325 mm CCD FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR 2006-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 50 95.3 0.064 11.25 1.6 112380 62.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.66 94.7 0.465 1.5 1.5
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 1Y0L 2.6 41.67 106731 5643 94.5 0.222 0.221 0.2505 0.244 0.2581 RANDOM 48.73
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] -0.28 0.27 -0.14 -1.22 -0.2 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.915 r_dihedral_angle_4_deg 19.367 r_dihedral_angle_3_deg 15.775 r_dihedral_angle_1_deg 6.545 r_angle_refined_deg 1.295 r_angle_other_deg 0.955 r_scangle_it 0.937 r_scbond_it 0.666 r_mcangle_it 0.416 r_symmetry_vdw_other 0.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.915 r_dihedral_angle_4_deg 19.367 r_dihedral_angle_3_deg 15.775 r_dihedral_angle_1_deg 6.545 r_angle_refined_deg 1.295 r_angle_other_deg 0.955 r_scangle_it 0.937 r_scbond_it 0.666 r_mcangle_it 0.416 r_symmetry_vdw_other 0.413 r_symmetry_hbond_refined 0.359 r_symmetry_vdw_refined 0.331 r_mcbond_it 0.317 r_metal_ion_refined 0.225 r_nbd_refined 0.206 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.181 r_mcbond_other 0.1 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.088 r_chiral_restr 0.073 r_symmetry_metal_ion_refined 0.044 r_bond_refined_d 0.012 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26768 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 73
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling