5JGI

X-ray structure of neuropilin-1 b1 domain complexed with M45 compound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.928920% PEG3350+0.2 M NH4Cl
Crystal Properties
Matthews coefficientSolvent content
2.1141.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.65α = 90
b = 89.203β = 98.71
c = 41.645γ = 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)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
11.3841.1695.70.03428.46.657512
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)
11.381.4700.1368.65.2

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 REPLACEMENTTHROUGHOUT1KEX1.3841.1654794271795.60.15190.151080.16914RANDOM13.705
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]
0.79-1.12-0.720.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.951
r_dihedral_angle_4_deg19.533
r_dihedral_angle_3_deg11.643
r_dihedral_angle_1_deg7.496
r_long_range_B_refined5.128
r_long_range_B_other4.893
r_scangle_other3.485
r_scbond_it2.287
r_scbond_other2.286
r_angle_refined_deg1.978
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.951
r_dihedral_angle_4_deg19.533
r_dihedral_angle_3_deg11.643
r_dihedral_angle_1_deg7.496
r_long_range_B_refined5.128
r_long_range_B_other4.893
r_scangle_other3.485
r_scbond_it2.287
r_scbond_other2.286
r_angle_refined_deg1.978
r_mcangle_it1.8
r_mcangle_other1.799
r_angle_other_deg1.424
r_mcbond_it1.184
r_mcbond_other1.183
r_chiral_restr0.129
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms339
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing