6WET

Crystal structures of human E-NPP 1: apo


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B56PDB entry 4B56

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
3.362.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.111α = 90
b = 158.885β = 90
c = 209.832γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-08-03MSINGLE 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
12.644.4231000.0530.99812.926.186202
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)
12.62.651000.9160.539114.5

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 4B562.644.486169446199.9620.2120.21040.244268.659
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]
2.2372.855-5.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.909
r_dihedral_angle_1_deg19.331
r_dihedral_angle_4_deg18.328
r_dihedral_angle_3_deg16.057
r_lrange_it11.668
r_lrange_other11.668
r_scangle_it7.136
r_scangle_other7.136
r_mcangle_it6.615
r_mcangle_other6.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.909
r_dihedral_angle_1_deg19.331
r_dihedral_angle_4_deg18.328
r_dihedral_angle_3_deg16.057
r_lrange_it11.668
r_lrange_other11.668
r_scangle_it7.136
r_scangle_other7.136
r_mcangle_it6.615
r_mcangle_other6.614
r_scbond_it4.525
r_scbond_other4.524
r_mcbond_it4.254
r_mcbond_other4.254
r_angle_refined_deg1.37
r_angle_other_deg1.192
r_symmetry_nbd_refined0.269
r_nbd_other0.268
r_symmetry_xyhbond_nbd_refined0.243
r_metal_ion_refined0.218
r_nbd_refined0.204
r_symmetry_nbd_other0.178
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.141
r_symmetry_xyhbond_nbd_other0.125
r_ncsr_local_group_10.105
r_symmetry_nbtor_other0.082
r_chiral_restr0.058
r_bond_refined_d0.005
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 Atoms12653
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing