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Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OP3 pdb entry 1op3 with carbohydrate removed from the Fab binding site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 1.33M Na/K phosphate, 0.2M isopropanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal Properties Matthews coefficient Solvent content 3.33 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.264 α = 90 b = 171.348 β = 105.64 c = 119.568 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 ADSC QUANTUM 4 2003-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 48.7 98.2 0.115 9.8 3.1 62018 62018 -3 58.9
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 2.8 2.85 97.9 0.476 2.5 3.1 3095
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 (All) 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 pdb entry 1op3 with carbohydrate removed from the Fab binding site 2.8 48.7 58837 58837 3138 98.16 0.236 0.236 0.23396 0.279 0.27461 0.3033 RANDOM 69.115
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] 9.14 7.85 -5.87 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.125 r_dihedral_angle_4_deg 18.271 r_dihedral_angle_3_deg 15.499 r_dihedral_angle_1_deg 5.266 r_angle_refined_deg 1.014 r_scangle_it 0.677 r_scbond_it 0.409 r_nbtor_refined 0.295 r_mcangle_it 0.272 r_nbd_refined 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.125 r_dihedral_angle_4_deg 18.271 r_dihedral_angle_3_deg 15.499 r_dihedral_angle_1_deg 5.266 r_angle_refined_deg 1.014 r_scangle_it 0.677 r_scbond_it 0.409 r_nbtor_refined 0.295 r_mcangle_it 0.272 r_nbd_refined 0.179 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.17 r_mcbond_it 0.156 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13685 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing