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Engineering the Species-Specificity of an Inhibitory Antibody Targeting a Modulator of Tumor Stroma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 5% w/v dimethyl sulfoxide, 0.1 M sodium acetate, pH 4.6, 7% w/v PEG monomethyl ether 2 kD
Crystal Properties Matthews coefficient Solvent content 2.21 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.48 α = 90 b = 116.375 β = 103.09 c = 50.023 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 IMAGE PLATE RIGAKU RAXIS IV++ 2012-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.05 50 95.8 0.063 0.063 11.3 3.7 28528 -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 2.05 2.09 79.2 0.318 2.2 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3Q6O 2.05 28.513 1.4 28485 1957 95.61 0.2045 0.201 0.206 0.2523 0.2545 random selection 31.5
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.9 f_angle_d 1.275 f_chiral_restr 0.094 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3707 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing