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Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293 50 mM Tris-HCl, 25% PEG 3350, 0.1 mM EDTA, pH8.3
Crystal Properties Matthews coefficient Solvent content 1.93 36.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.986 α = 90 b = 36.553 β = 91.5 c = 111.986 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 225 mm CCD 2017-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 50 100 0.155 0.167 0.063 10.9 6.9 59706
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.921 1.005 0.397 0.774 2.8 6.3
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 2DTM 1.9 50 56045 2993 99.98 0.197 0.19421 0.2014 0.24929 0.2525 RANDOM 32.642
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_4_deg 18.019 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_1_deg 7.279 r_long_range_B_refined 7.058 r_long_range_B_other 7.055 r_scangle_other 5.008 r_mcangle_it 4.311 r_mcangle_other 4.31 r_scbond_other 3.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_4_deg 18.019 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_1_deg 7.279 r_long_range_B_refined 7.058 r_long_range_B_other 7.055 r_scangle_other 5.008 r_mcangle_it 4.311 r_mcangle_other 4.31 r_scbond_other 3.348 r_scbond_it 3.347 r_mcbond_it 2.937 r_mcbond_other 2.933 r_angle_refined_deg 1.818 r_angle_other_deg 0.985 r_chiral_restr 0.197 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6754 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing