6FMC

Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277.1516 % w/v PEG3350 and 200 mM ammonium chloride
Crystal Properties
Matthews coefficientSolvent content
2.448.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.44α = 90
b = 43.44β = 90
c = 91.23γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.813010SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
10.943.4494.50.0570.99810.553.3117690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.90.9570.70.4780.795

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 REPLACEMENTTHROUGHOUT1KEX0.943.44111866602794.670.110150.108940.13207RANDOM16.789
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.593
r_sphericity_free34.773
r_dihedral_angle_4_deg18.625
r_dihedral_angle_3_deg14.861
r_sphericity_bonded13.469
r_rigid_bond_restr9.893
r_dihedral_angle_1_deg7.652
r_long_range_B_refined6.334
r_long_range_B_other4.551
r_scangle_other3.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.593
r_sphericity_free34.773
r_dihedral_angle_4_deg18.625
r_dihedral_angle_3_deg14.861
r_sphericity_bonded13.469
r_rigid_bond_restr9.893
r_dihedral_angle_1_deg7.652
r_long_range_B_refined6.334
r_long_range_B_other4.551
r_scangle_other3.405
r_angle_other_deg3.282
r_scbond_it3.011
r_scbond_other3.009
r_angle_refined_deg2.647
r_mcangle_it1.576
r_mcangle_other1.575
r_mcbond_it1.2
r_mcbond_other1.197
r_chiral_restr0.104
r_bond_refined_d0.02
r_gen_planes_other0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1261
Nucleic Acid Atoms
Solvent Atoms472
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing