6YLZ

X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant of PNP-oxidase from E. coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G76 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM KPHO pH 7,5, 5 mM 2-mercaptoethanol, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.8857.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.776α = 90
b = 63.776β = 90
c = 124.727γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.968620DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.55855.233980.130.1340.030.99913.619.741877
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)
11.5581.585980.8030.4440.911.91

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-VALUE1G761.55855.23241608206197.3510.1720.17060.202233.06
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]
0.7780.3890.778-2.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.336
r_dihedral_angle_3_deg13.685
r_dihedral_angle_4_deg13.185
r_lrange_it8.08
r_lrange_other7.994
r_dihedral_angle_1_deg7.082
r_scangle_it6.075
r_scangle_other6.061
r_mcangle_other4.181
r_mcangle_it4.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.336
r_dihedral_angle_3_deg13.685
r_dihedral_angle_4_deg13.185
r_lrange_it8.08
r_lrange_other7.994
r_dihedral_angle_1_deg7.082
r_scangle_it6.075
r_scangle_other6.061
r_mcangle_other4.181
r_mcangle_it4.178
r_scbond_it4.036
r_scbond_other3.972
r_mcbond_it3.017
r_mcbond_other3.008
r_angle_refined_deg1.721
r_angle_other_deg1.428
r_nbd_refined0.272
r_xyhbond_nbd_refined0.237
r_symmetry_xyhbond_nbd_refined0.204
r_symmetry_nbd_other0.196
r_nbd_other0.193
r_nbtor_refined0.175
r_symmetry_nbd_refined0.173
r_symmetry_nbtor_other0.084
r_chiral_restr0.083
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1748
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata collection
autoPROCdata processing
XDSdata reduction
XDSdata scaling
Aimlessdata processing
MOLREPphasing
Cootmodel building