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Crystal structure of P20.1 Fab fragment in complex with its antigen peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NC4 PDB ENTRY 1NC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 20-23% (wt/vol) PEG 3000, 0.1M Sodium acetate (pH4.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.045 α = 99.93 b = 65.271 β = 93.5 c = 85.03 γ = 96.46
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE DIP-6040 2006-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 1.8 46.78 97.8 0.042 10.3 2.5 76301 -3 21.64
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 1.8 1.9 95.3 0.234 3.2 2.5 10894
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 PDB ENTRY 1NC4 1.8 46.78 72513 3774 97.8 0.1735 0.1719 0.1723 0.2037 0.2052 RANDOM 28.28
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] 0.33 -0.58 -0.8 -0.28 0.8 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_1_deg 6.676 r_scangle_it 2.953 r_scbond_it 1.941 r_angle_refined_deg 1.47 r_mcangle_it 1.223 r_mcbond_it 0.758 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_1_deg 6.676 r_scangle_it 2.953 r_scbond_it 1.941 r_angle_refined_deg 1.47 r_mcangle_it 1.223 r_mcbond_it 0.758 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6441 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing