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Structure of IgG1 Fab fragment in complex with Biotincytidinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished in house Fab fragment structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.15M ammonium sulfate, 0.1M MES, 15%PEG 4000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.094 α = 90 b = 119.62 β = 117.15 c = 96.181 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 110 PIXEL PSI PILATUS 6M 2011-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
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 2.35 119 99.9 0.057 10.29 3.47 74713 74645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.4 99.9 0.65 3.53 3658
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished in house Fab fragment structure 2.5 119 62797 58977 3132 99.91 0.22799 0.22547 0.2268 0.27446 0.2718 RANDOM 78.96
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] -1.24 4.17 -2.72 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.185 r_dihedral_angle_4_deg 14.784 r_dihedral_angle_3_deg 13.842 r_dihedral_angle_1_deg 5.638 r_long_range_B_refined 5.383 r_long_range_B_other 5.342 r_mcangle_it 1.929 r_mcangle_other 1.929 r_scangle_other 1.555 r_mcbond_it 1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.185 r_dihedral_angle_4_deg 14.784 r_dihedral_angle_3_deg 13.842 r_dihedral_angle_1_deg 5.638 r_long_range_B_refined 5.383 r_long_range_B_other 5.342 r_mcangle_it 1.929 r_mcangle_other 1.929 r_scangle_other 1.555 r_mcbond_it 1.109 r_mcbond_other 1.108 r_angle_refined_deg 0.994 r_scbond_it 0.966 r_scbond_other 0.887 r_angle_other_deg 0.641 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13109 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 105
Software Software Software Name Purpose DA+ data collection PHASER phasing REFMAC refinement XDS data reduction SADABS data scaling