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Structure of Herceptin Fab without antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8Z PDB entry 1N8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 200 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, 25% v/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.99 α = 113.59 b = 78.89 β = 92.78 c = 85.14 γ = 101.68
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 315r 2016-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 43.61 90.5 0.115 0.137 0.073 0.977 7.3 3.4 19572
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 92.5 0.385 0.455 0.24 0.862 3.4
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 1N8Z 2.8 42.08 18615 956 90.46 0.2538 0.2511 0.2537 0.3062 0.3068 RANDOM 53.676
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] -3.25 0.81 -2.43 5.35 3.58 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 21.7 r_dihedral_angle_3_deg 17.177 r_dihedral_angle_1_deg 7.623 r_angle_refined_deg 1.625 r_angle_other_deg 1.488 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_bond_other_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 21.7 r_dihedral_angle_3_deg 17.177 r_dihedral_angle_1_deg 7.623 r_angle_refined_deg 1.625 r_angle_other_deg 1.488 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5738 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction