6WEU

Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate


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
3.3262.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.01α = 90
b = 160.143β = 90
c = 209.632γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953731Australian 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
12.6547.6131000.0550.99712.126.982015
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)
12.652.70.8160.5081

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 6WET2.6547.5781930420899.9620.2090.2070.23960.145
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]
1.4473.265-4.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_1_deg19.328
r_dihedral_angle_4_deg17.856
r_dihedral_angle_3_deg15.516
r_lrange_other10.996
r_lrange_it10.995
r_scangle_it6.201
r_scangle_other6.201
r_mcangle_it5.723
r_mcangle_other5.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_1_deg19.328
r_dihedral_angle_4_deg17.856
r_dihedral_angle_3_deg15.516
r_lrange_other10.996
r_lrange_it10.995
r_scangle_it6.201
r_scangle_other6.201
r_mcangle_it5.723
r_mcangle_other5.722
r_scbond_it3.834
r_scbond_other3.834
r_mcbond_it3.567
r_mcbond_other3.566
r_angle_refined_deg1.356
r_angle_other_deg1.185
r_metal_ion_refined0.322
r_nbd_other0.256
r_nbd_refined0.197
r_symmetry_nbd_refined0.193
r_symmetry_nbd_other0.182
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.129
r_symmetry_xyhbond_nbd_other0.112
r_ncsr_local_group_10.102
r_symmetry_nbtor_other0.076
r_chiral_restr0.055
r_symmetry_xyhbond_nbd_refined0.03
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12698
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing