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Crystal structure of the hydrolytic antibody Fab 9C10
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 6.5 277 30% PEG MME 550, 0.05M calcium chloride, 0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.436 α = 90 b = 60.142 β = 108.43 c = 56.08 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 2011-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 50 99.9 0.047 16.88 7.4 27974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.9 0.344 2.32
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 2.11 50 26565 1409 99.23 0.17804 0.17481 0.1843 0.23691 0.2402 RANDOM 38.709
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.089 r_dihedral_angle_3_deg 16.105 r_dihedral_angle_4_deg 15.375 r_long_range_B_refined 8.561 r_long_range_B_other 8.56 r_dihedral_angle_1_deg 7.378 r_scangle_other 6.633 r_mcangle_other 4.698 r_mcangle_it 4.696 r_scbond_it 4.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.089 r_dihedral_angle_3_deg 16.105 r_dihedral_angle_4_deg 15.375 r_long_range_B_refined 8.561 r_long_range_B_other 8.56 r_dihedral_angle_1_deg 7.378 r_scangle_other 6.633 r_mcangle_other 4.698 r_mcangle_it 4.696 r_scbond_it 4.423 r_scbond_other 4.423 r_mcbond_it 3.269 r_mcbond_other 3.265 r_angle_refined_deg 1.878 r_angle_other_deg 0.898 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 3377 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing