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Fab fragment of calcium-dependent antigen binding antibody, 6RL#9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZA6 1ZA6 for VH, CL, and CH1 regions, 2A9M for VL region experimental model PDB 2A9M 1ZA6 for VH, CL, and CH1 regions, 2A9M for VL region
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20.0% PEG 4000, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.47 α = 90 b = 79.86 β = 90 c = 116.25 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 95 CCD ADSC QUANTUM 315r 2010-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 2.2 42.35 99.99 0.113 14.8 7.12 22199 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.628 3.4 7.25
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 1ZA6 for VH, CL, and CH1 regions, 2A9M for VL region 2.2 25 21023 1162 99.9 0.2145 0.2114 0.2134 0.2724 0.274 RANDOM 27.373
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] -0.17 0.69 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.494 r_dihedral_angle_4_deg 19.516 r_dihedral_angle_3_deg 14.414 r_dihedral_angle_1_deg 5.906 r_mcangle_it 1.496 r_angle_refined_deg 1.212 r_mcbond_it 0.821 r_scbond_it 0.681 r_chiral_restr 0.068 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.494 r_dihedral_angle_4_deg 19.516 r_dihedral_angle_3_deg 14.414 r_dihedral_angle_1_deg 5.906 r_mcangle_it 1.496 r_angle_refined_deg 1.212 r_mcbond_it 0.821 r_scbond_it 0.681 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3195 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data processing XDS data reduction XSCALE data scaling Coot model building PHASER phasing