6WEV

Crystal structures of human E-NPP 1: bound to N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}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
3.2662.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.278α = 90
b = 158.993β = 90
c = 209.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953736Australian 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
12.947.32299.90.0850.9939.92661713
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)
12.92.980.740.5691.1

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 6WET2.947.2861629312299.8930.2130.21120.253462.639
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]
1.9454.251-6.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.626
r_dihedral_angle_1_deg20.716
r_dihedral_angle_4_deg18.102
r_dihedral_angle_3_deg16.288
r_lrange_it11.852
r_lrange_other11.849
r_mcangle_it7.04
r_mcangle_other7.039
r_scangle_it7.013
r_scangle_other7.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.626
r_dihedral_angle_1_deg20.716
r_dihedral_angle_4_deg18.102
r_dihedral_angle_3_deg16.288
r_lrange_it11.852
r_lrange_other11.849
r_mcangle_it7.04
r_mcangle_other7.039
r_scangle_it7.013
r_scangle_other7.008
r_mcbond_it4.436
r_mcbond_other4.436
r_scbond_it4.381
r_scbond_other4.346
r_dihedral_angle_other_3_deg3.466
r_angle_refined_deg1.458
r_angle_other_deg1.233
r_symmetry_nbd_refined0.208
r_nbd_refined0.207
r_symmetry_nbd_other0.18
r_nbd_other0.18
r_nbtor_refined0.169
r_metal_ion_refined0.157
r_xyhbond_nbd_refined0.148
r_ncsr_local_group_10.095
r_chiral_restr0.084
r_symmetry_nbtor_other0.079
r_symmetry_xyhbond_nbd_refined0.071
r_symmetry_xyhbond_nbd_other0.015
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12734
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms278

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing