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Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Gln 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 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.116 α = 90 b = 86.22 β = 90 c = 113.643 γ = 90
Symmetry Space Group P 21 21 21
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 300 mm CCD ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY 2006-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9793 APS 23-ID-D
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 2.18 50 91.8 0.093 15.9 3.2 39309 -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 2.18 2.25 87.8 0.613 2.2 3.2
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 2.18 31.27 37589 1994 91.89 0.20404 0.2014 0.2122 0.25583 0.2638 RANDOM 43.444
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] 0.03 0.14 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.324 r_dihedral_angle_4_deg 16.337 r_dihedral_angle_3_deg 16.063 r_dihedral_angle_1_deg 6.84 r_scangle_it 3.486 r_scbond_it 2.694 r_angle_refined_deg 1.527 r_mcbond_it 1.461 r_mcangle_it 1.249 r_angle_other_deg 0.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.324 r_dihedral_angle_4_deg 16.337 r_dihedral_angle_3_deg 16.063 r_dihedral_angle_1_deg 6.84 r_scangle_it 3.486 r_scbond_it 2.694 r_angle_refined_deg 1.527 r_mcbond_it 1.461 r_mcangle_it 1.249 r_angle_other_deg 0.867 r_symmetry_hbond_refined 0.283 r_symmetry_vdw_refined 0.24 r_symmetry_vdw_other 0.222 r_nbd_other 0.204 r_nbd_refined 0.192 r_nbtor_refined 0.182 r_mcbond_other 0.157 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.092 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_bond_other_d 0.008 r_gen_planes_refined 0.005 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 6538 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 38
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling