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Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HFT PDB ENTRIES 2HFT AND 1JPT experimental model PDB 1JPT PDB ENTRIES 2HFT AND 1JPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2-propanol, PEG4000, HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.85 67.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.054 α = 90 b = 265.996 β = 90 c = 42.254 γ = 90
Symmetry Space Group P 21 21 2
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 2002-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.1 37.1 94 0.087 69013 64872 3 19.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.2 81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2HFT AND 1JPT 2.1 37.01 3 69013 62792 6352 90.6 0.2 0.196 0.196 0.2118 0.227 RANDOM 32.3
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] 1.43 1.86 -3.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.1 c_scangle_it 4.89 c_mcangle_it 4.36 c_scbond_it 3.64 c_mcbond_it 3 c_angle_deg 1.6 c_improper_angle_d 0.98 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.1 c_scangle_it 4.89 c_mcangle_it 4.36 c_scbond_it 3.64 c_mcbond_it 3 c_angle_deg 1.6 c_improper_angle_d 0.98 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4913 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms
Software Software Software Name Purpose CNS refinement MOSFLM data reduction CCP4 data scaling CNS phasing