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Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Ala mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GJZ PDB entry 2GJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 25% PEG 3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.602 α = 90 b = 87.021 β = 91.34 c = 84.401 γ = 90
Symmetry Space Group P 1 21 1
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 2006-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 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 2.2 50 99.8 0.072 22.3 3.5 43563 -3
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 2.2 2.25 99.8 0.506 2.4 3.4
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 2GJZ 2.2 42.84 41378 2256 99.69 0.22786 0.22496 0.2375 0.28139 0.2978 RANDOM 27.708
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] 4.04 -0.06 -3.6 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 20.331 r_dihedral_angle_3_deg 16.52 r_dihedral_angle_1_deg 6.792 r_scangle_it 1.921 r_angle_refined_deg 1.421 r_scbond_it 1.343 r_angle_other_deg 0.885 r_mcangle_it 0.785 r_mcbond_it 0.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 20.331 r_dihedral_angle_3_deg 16.52 r_dihedral_angle_1_deg 6.792 r_scangle_it 1.921 r_angle_refined_deg 1.421 r_scbond_it 1.343 r_angle_other_deg 0.885 r_mcangle_it 0.785 r_mcbond_it 0.658 r_nbd_other 0.199 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.183 r_nbtor_refined 0.179 r_symmetry_vdw_other 0.169 r_xyhbond_nbd_refined 0.159 r_mcbond_other 0.125 r_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 6540 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 38
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling