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Crystal structure analysis of the anti-(4-hydroxy-3-nitrophenyl)- acetyl murine germline antibody BBE6.12H3 Fab fragment in complex with a phage display derived dodecapeptide DLWTTAIPTIPS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE FAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 0.05M TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350., pH 7.1
Crystal Properties Matthews coefficient Solvent content 2.02 39.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.01 α = 90 b = 63.62 β = 90.4 c = 113.38 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 287 CCD MARMOSAIC 225 mm CCD BENT COLLIMATING MIRROR AND TOROID 2009-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.7 50 100 0.07 11.3 5.1 11098 28.3
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 2.7 8.5 100 0.28 4.1 5.1
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 NATIVE FAB 2.7 50 9995 1081 90.1 0.2305 0.2305 0.2259 0.2477 0.2849 RANDOM 42.4
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] -12.165 -1.132 26.388 -14.223
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 28.5 c_angle_deg 1.96434 c_improper_angle_d 1.3 c_bond_d 0.009918 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 28.5 c_angle_deg 1.96434 c_improper_angle_d 1.3 c_bond_d 0.009918 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 3294 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling MOLREP phasing