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Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V7N PDB ENTRY 2V7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG4000, 0.1M MOPS, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.59 65.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.561 α = 90 b = 83.009 β = 103.38 c = 91.824 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 90 CCD MARRESEARCH BENT MIRRORS 2006-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97640 SLS X06SA
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 1.75 50 97.5 0.074 12.7 3.1 130926
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 1.75 1.81 85.8 0.306 2.5 11474
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 2V7N 1.75 35.94 130868 1286 100 0.183 0.182 0.1968 0.201 0.2089 RANDOM 25.544
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] -0.03 -1.06 0.47 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 17.037 r_dihedral_angle_3_deg 12.371 r_dihedral_angle_1_deg 7.351 r_sphericity_free 6.899 r_sphericity_bonded 5.685 r_scangle_it 4.122 r_scbond_it 2.914 r_mcangle_it 2.174 r_rigid_bond_restr 1.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 17.037 r_dihedral_angle_3_deg 12.371 r_dihedral_angle_1_deg 7.351 r_sphericity_free 6.899 r_sphericity_bonded 5.685 r_scangle_it 4.122 r_scbond_it 2.914 r_mcangle_it 2.174 r_rigid_bond_restr 1.984 r_angle_refined_deg 1.524 r_mcbond_it 1.414 r_nbtor_refined 0.304 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6564 Nucleic Acid Atoms Solvent Atoms 767 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection