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Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEX 1KEX (b1 domain), 2FJH (Fab) experimental model PDB 2FJH 1KEX (b1 domain), 2FJH (Fab)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 25% PEG 1500, 4% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.06 59.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 214.115 α = 90 b = 214.115 β = 90 c = 45.465 γ = 120
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 MARMOSAIC 325 mm CCD 2006-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1
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 2.2 50 99 0.096 14.3 4.4 39195 41.1
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 2.2 2.28 98 0.485 2.2 3.6 3893
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 1KEX (b1 domain), 2FJH (Fab) 2.2 20 37085 1976 99.06 0.162 0.159 0.1686 0.207 0.2114 RANDOM 33.243
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] 0.16 0.08 0.16 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.918 r_dihedral_angle_4_deg 21.285 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_1_deg 6.906 r_scangle_it 5.051 r_mcangle_it 4.335 r_scbond_it 3.61 r_mcbond_it 3.523 r_angle_refined_deg 1.427 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.918 r_dihedral_angle_4_deg 21.285 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_1_deg 6.906 r_scangle_it 5.051 r_mcangle_it 4.335 r_scbond_it 3.61 r_mcbond_it 3.523 r_angle_refined_deg 1.427 r_angle_other_deg 0.886 r_mcbond_other 0.713 r_symmetry_vdw_other 0.197 r_nbd_other 0.196 r_nbd_refined 0.178 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.16 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.09 r_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4540 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction