6WEW

Crystal structures of human E-NPP 1: bound to N-{4-[(7-methoxyquinolin-4-yl)oxy]phenyl}sulfuric diamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6WETPDB entry 6WET

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2817.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate
Crystal Properties
Matthews coefficientSolvent content
3.3663.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.131α = 90
b = 161.578β = 90
c = 209.978γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953730Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim 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
12.7347.9671000.1050.998.411.876020
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.732.790.7650.5481.3

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-VALUEPDB entry 6WET2.7347.9275942377199.9550.2120.21020.240951.507
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]
0.9822.553-3.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_1_deg21.176
r_dihedral_angle_4_deg17.777
r_dihedral_angle_3_deg15.441
r_lrange_other10.499
r_lrange_it10.497
r_scangle_other5.637
r_scangle_it5.636
r_mcangle_it5.385
r_mcangle_other5.385
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_1_deg21.176
r_dihedral_angle_4_deg17.777
r_dihedral_angle_3_deg15.441
r_lrange_other10.499
r_lrange_it10.497
r_scangle_other5.637
r_scangle_it5.636
r_mcangle_it5.385
r_mcangle_other5.385
r_scbond_other3.435
r_scbond_it3.434
r_mcbond_it3.29
r_mcbond_other3.289
r_angle_refined_deg1.393
r_angle_other_deg1.187
r_symmetry_xyhbond_nbd_refined0.245
r_nbd_other0.23
r_symmetry_nbd_refined0.218
r_nbd_refined0.2
r_symmetry_nbd_other0.177
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.139
r_metal_ion_refined0.113
r_ncsr_local_group_10.089
r_symmetry_nbtor_other0.077
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_symmetry_xyhbond_nbd_other0.004
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12688
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms308

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing