☰ Navigation Tabs
Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQK PDB entry 2QQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.8 67.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.406 α = 90 b = 121.406 β = 90 c = 202.717 γ = 120
Symmetry Space Group P 32 2 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 CCD ADSC QUANTUM 315 2006-04-07 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 3.1 50 99.6 0.061 18.3 3.8 31929 102
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 3.1 3.21 98.9 0.515 2.6 3.6 3101
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 2QQK 3.1 30 30265 1610 99.69 0.19 0.188 0.232 0.2733 RANDOM 97.086
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] -2.13 -1.07 -2.13 3.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_3_deg 18.277 r_dihedral_angle_4_deg 17.306 r_dihedral_angle_1_deg 7.316 r_mcangle_it 3.85 r_scangle_it 3.36 r_mcbond_it 2.754 r_scbond_it 2.212 r_angle_refined_deg 1.309 r_angle_other_deg 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_3_deg 18.277 r_dihedral_angle_4_deg 17.306 r_dihedral_angle_1_deg 7.316 r_mcangle_it 3.85 r_scangle_it 3.36 r_mcbond_it 2.754 r_scbond_it 2.212 r_angle_refined_deg 1.309 r_angle_other_deg 0.828 r_mcbond_other 0.452 r_symmetry_vdw_other 0.206 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.204 r_nbd_other 0.191 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.157 r_nbtor_other 0.087 r_chiral_restr 0.073 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 7740 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing