5JGQ

X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KEX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.928918%PEG3350+0.2M NH4Cl
Crystal Properties
Matthews coefficientSolvent content
2.0941.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.789α = 90
b = 89.568β = 98.57
c = 41.385γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.640.92970.0470.99810.53.137578
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)
11.61.6375.30.44221.9

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 REPLACEMENTTHROUGHOUT1kex1.644.7835677185396.880.162190.160560.19304RANDOM19.591
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]
0.1-1.51-0.010.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.434
r_dihedral_angle_4_deg19.489
r_dihedral_angle_3_deg11.998
r_dihedral_angle_1_deg7.188
r_long_range_B_refined5.327
r_long_range_B_other5.326
r_scangle_other3.593
r_scbond_it2.331
r_scbond_other2.33
r_mcangle_it2.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.434
r_dihedral_angle_4_deg19.489
r_dihedral_angle_3_deg11.998
r_dihedral_angle_1_deg7.188
r_long_range_B_refined5.327
r_long_range_B_other5.326
r_scangle_other3.593
r_scbond_it2.331
r_scbond_other2.33
r_mcangle_it2.153
r_mcangle_other2.152
r_angle_refined_deg1.864
r_angle_other_deg1.479
r_mcbond_it1.456
r_mcbond_other1.452
r_chiral_restr0.127
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.008
r_gen_planes_other0.007
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 Atoms2489
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing