6WFJ

Crystal structures of human E-NPP 1: apo


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
3.362.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.951α = 90
b = 159.687β = 90
c = 209.245γ = 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
12.547.48799.90.0410.99915.126.196772
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)
12.52.540.5670.651.3

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 6WET2.547.4496689484199.8510.2010.19940.222360.345
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]
2.031.996-4.025
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.684
r_dihedral_angle_1_deg22.967
r_dihedral_angle_4_deg17.136
r_dihedral_angle_3_deg15.13
r_lrange_other10.14
r_lrange_it10.137
r_scangle_it5.505
r_scangle_other5.505
r_mcangle_it5.012
r_mcangle_other5.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.684
r_dihedral_angle_1_deg22.967
r_dihedral_angle_4_deg17.136
r_dihedral_angle_3_deg15.13
r_lrange_other10.14
r_lrange_it10.137
r_scangle_it5.505
r_scangle_other5.505
r_mcangle_it5.012
r_mcangle_other5.012
r_scbond_it3.357
r_scbond_other3.357
r_mcbond_it3.091
r_mcbond_other3.09
r_angle_refined_deg1.373
r_angle_other_deg1.218
r_nbd_refined0.196
r_nbd_other0.182
r_symmetry_nbd_other0.175
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.141
r_metal_ion_refined0.117
r_ncsr_local_group_10.093
r_symmetry_nbtor_other0.078
r_chiral_restr0.071
r_symmetry_nbd_refined0.071
r_symmetry_xyhbond_nbd_other0.044
r_symmetry_xyhbond_nbd_refined0.024
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 Atoms12750
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms311

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing