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Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289.15 25 % PEG 550 MME, 0.1 M MES pH 6.5, 0.01 M ZnSO4
Crystal Properties Matthews coefficient Solvent content 3.26 62.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.39 α = 90 b = 105.27 β = 90 c = 45.75 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 291 CCD MARMOSAIC 225 mm CCD 2012-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 1.8 36.13 99.9 0.052 16.5 4.6 22736
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 1.8 1.9 0.23
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 2QQJ 1.8 36.13 21563 1161 99.89 0.1791 0.17707 0.1875 0.2173 0.2263 RANDOM 25.45
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] -0.1 0.35 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.685 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 14.134 r_long_range_B_refined 7.734 r_long_range_B_other 7.733 r_dihedral_angle_1_deg 7.535 r_scangle_other 4.337 r_scbond_other 2.792 r_scbond_it 2.791 r_mcangle_it 2.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.685 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 14.134 r_long_range_B_refined 7.734 r_long_range_B_other 7.733 r_dihedral_angle_1_deg 7.535 r_scangle_other 4.337 r_scbond_other 2.792 r_scbond_it 2.791 r_mcangle_it 2.492 r_mcangle_other 2.491 r_mcbond_it 1.869 r_mcbond_other 1.862 r_angle_refined_deg 1.753 r_angle_other_deg 1.015 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1250 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Coot model building SCALA data scaling MOSFLM data reduction PHASER phasing