5IJR

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.929328% w/v PEG3350, 0.2 M AmCl
Crystal Properties
Matthews coefficientSolvent content
2.0539.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.139α = 90
b = 88.936β = 96.73
c = 40.962γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-02-23MSINGLE 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
11.5240.6895.40.048122.86.641807
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)
11.521.5567.80.512.85.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5240.6839714209395.290.182640.18110.21298RANDOM20.083
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]
0.46-1.08-1.571.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.801
r_dihedral_angle_4_deg20.695
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg7.391
r_long_range_B_refined5.172
r_long_range_B_other5.171
r_scangle_other2.541
r_angle_refined_deg1.883
r_mcangle_it1.651
r_mcangle_other1.651
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.801
r_dihedral_angle_4_deg20.695
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg7.391
r_long_range_B_refined5.172
r_long_range_B_other5.171
r_scangle_other2.541
r_angle_refined_deg1.883
r_mcangle_it1.651
r_mcangle_other1.651
r_scbond_it1.626
r_scbond_other1.625
r_angle_other_deg1.543
r_mcbond_it0.983
r_mcbond_other0.983
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.009
r_gen_planes_other0.008
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 Atoms2475
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing