5L73

MAM domain of human neuropilin-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2890.06 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 coefficientSolvent content
2.1442.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.172α = 90
b = 59.558β = 90
c = 136.654γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9895DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2446.1798.30.11166.218498
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.240.41

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2c9a2.2468.331749296497.980.174710.171790.22827RANDOM25.33
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]
-0.370.090.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.801
r_dihedral_angle_4_deg18.404
r_dihedral_angle_3_deg15.215
r_dihedral_angle_1_deg10.989
r_long_range_B_refined6.141
r_long_range_B_other6.14
r_scangle_other3.894
r_mcangle_other3.561
r_mcangle_it3.558
r_scbond_it2.234
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.801
r_dihedral_angle_4_deg18.404
r_dihedral_angle_3_deg15.215
r_dihedral_angle_1_deg10.989
r_long_range_B_refined6.141
r_long_range_B_other6.14
r_scangle_other3.894
r_mcangle_other3.561
r_mcangle_it3.558
r_scbond_it2.234
r_scbond_other2.232
r_mcbond_it2.071
r_mcbond_other2.034
r_angle_refined_deg1.553
r_angle_other_deg0.951
r_chiral_restr0.101
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2798
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing