☰ Navigation Tabs
MAM domain of human neuropilin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.06 M MgCl2
0.06 M CaCl2
0.1 M Tris (base), 0.1 M
BICINE pH 8.0
12.5 % MPD
12.5 % PEG 1000
12.5 % w/v PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.172 α = 90 b = 59.558 β = 90 c = 136.654 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M-F 2016-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9895 Diamond I04
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 2.24 46.17 98.3 0.11 16 6.2 18498
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 2.24 0.41
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 2c9a 2.24 68.33 17492 964 97.98 0.17471 0.17179 0.22827 0.2152 RANDOM 25.33
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] -0.37 0.09 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.801 r_dihedral_angle_4_deg 18.404 r_dihedral_angle_3_deg 15.215 r_dihedral_angle_1_deg 10.989 r_long_range_B_refined 6.141 r_long_range_B_other 6.14 r_scangle_other 3.894 r_mcangle_other 3.561 r_mcangle_it 3.558 r_scbond_it 2.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.801 r_dihedral_angle_4_deg 18.404 r_dihedral_angle_3_deg 15.215 r_dihedral_angle_1_deg 10.989 r_long_range_B_refined 6.141 r_long_range_B_other 6.14 r_scangle_other 3.894 r_mcangle_other 3.561 r_mcangle_it 3.558 r_scbond_it 2.234 r_scbond_other 2.232 r_mcbond_it 2.071 r_mcbond_other 2.034 r_angle_refined_deg 1.553 r_angle_other_deg 0.951 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 2798 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing