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Dual specific bH1 Fab in complex with VEGF
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 7.5 292 For crystallization of the Fab/VEGF (8-109) complex, equal volumes of protein complex solution (10.6 mg/ml protein, 300 mM NaCl, 25 mM Tris-HCl pH 7.5) and crystallization buffer containing 0.15 D, L Malic Acid pH 7.0, 20% PEG3350 were mixed and equilibrated at 19 C. Prior to data collection the crystals were cryo-protected by transfer between drops containing 5%, 10% and 15% Glycerol in artificial mother liquor, followed by flash freeze in liquid nitrogen, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.17 61.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.6 α = 90 b = 197.978 β = 90 c = 77.65 γ = 90
Symmetry Space Group C 2 2 21
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 315 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.8 0.09 16 6.2 24755 24705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 100 0.658 3 6.2 2419
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1N8Z 2.6 30 24225 1248 99.81 0.197 0.194 0.252 0.2893 RANDOM 40.479
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] -1.01 -0.56 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.833 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_3_deg 15.219 r_dihedral_angle_1_deg 6.122 r_scangle_it 3.823 r_mcangle_it 3.645 r_mcbond_it 2.769 r_scbond_it 2.67 r_angle_refined_deg 1.255 r_angle_other_deg 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.833 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_3_deg 15.219 r_dihedral_angle_1_deg 6.122 r_scangle_it 3.823 r_mcangle_it 3.645 r_mcbond_it 2.769 r_scbond_it 2.67 r_angle_refined_deg 1.255 r_angle_other_deg 0.805 r_mcbond_other 0.517 r_symmetry_vdw_refined 0.346 r_nbd_other 0.19 r_nbd_refined 0.185 r_nbtor_refined 0.181 r_symmetry_vdw_other 0.14 r_xyhbond_nbd_refined 0.127 r_nbtor_other 0.084 r_symmetry_hbond_refined 0.075 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4072 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection