6SH1

Crystal structure of substrate-free human neprilysin E584D.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GID 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION291.15Potassium nitrate, sodium bromide, Bis-Tris propane, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.346.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.14α = 90
b = 99.745β = 106.231
c = 100.119γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.169.2299.90.9926.66.9576297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.140.4641

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6GID2.169.2283801426899.9170.2210.21840.261440.443
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]
-1.422-2.1412.931-0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.974
r_dihedral_angle_4_deg14.686
r_dihedral_angle_3_deg14.516
r_dihedral_angle_1_deg5.633
r_lrange_it4.611
r_lrange_other4.584
r_scangle_it2.96
r_scangle_other2.96
r_mcangle_it2.586
r_mcangle_other2.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.974
r_dihedral_angle_4_deg14.686
r_dihedral_angle_3_deg14.516
r_dihedral_angle_1_deg5.633
r_lrange_it4.611
r_lrange_other4.584
r_scangle_it2.96
r_scangle_other2.96
r_mcangle_it2.586
r_mcangle_other2.586
r_angle_other_deg2.349
r_scbond_it1.749
r_scbond_other1.749
r_mcbond_it1.583
r_mcbond_other1.583
r_angle_refined_deg1.212
r_symmetry_nbd_other0.202
r_nbd_other0.18
r_nbd_refined0.175
r_nbtor_refined0.154
r_xyhbond_nbd_refined0.15
r_symmetry_xyhbond_nbd_refined0.134
r_symmetry_nbd_refined0.119
r_metal_ion_refined0.106
r_symmetry_nbtor_other0.057
r_chiral_restr0.045
r_symmetry_xyhbond_nbd_other0.037
r_bond_other_d0.036
r_gen_planes_other0.004
r_bond_refined_d0.003
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11031
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing