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High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IGF PDB ENTRY 2IGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 THE PRE-FORMED COMPLEX WAS CRYSTALLIZED FROM 17% PEG 4000, 50MM TRIS, 0.1MM EDTA, PH 8.3
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.906 α = 90 b = 61.662 β = 104.68 c = 66.673 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 293 IMAGE PLATE FUJI 1994-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
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 1.8 6 69 0.07 6.1 28513 2 4.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 2 44
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2IGF 1.8 6 27402 27402 3055 69 0.187 0.187 0.1851 0.246 0.2435 RANDOM 25.6
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] -0.69 -0.16 3.89 -3.2
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.1 c_angle_deg 1.5 c_improper_angle_d 0.96 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.1 c_angle_deg 1.5 c_improper_angle_d 0.96 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3349 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 48
Software Software Software Name Purpose WEIS data scaling PROTEIN data reduction X-PLOR model building CNS refinement WEIS data reduction PROTEIN data scaling X-PLOR phasing