6YMH

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


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
2.2645.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.164α = 90
b = 54.164β = 90
c = 271.968γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96828DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.41746.9071000.2170.0480.99911.920.117206
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)
12.4172.4591000.8750.3920.917.2

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-VALUE1G762.41746.9071718980099.8950.1930.18970.258859.324
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]
-1.799-0.9-1.7995.836
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.122
r_dihedral_angle_4_deg16.91
r_dihedral_angle_3_deg16.859
r_lrange_it7.621
r_lrange_other7.621
r_dihedral_angle_1_deg6.864
r_scangle_it5.2
r_scangle_other5.199
r_mcangle_it4.814
r_mcangle_other4.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.122
r_dihedral_angle_4_deg16.91
r_dihedral_angle_3_deg16.859
r_lrange_it7.621
r_lrange_other7.621
r_dihedral_angle_1_deg6.864
r_scangle_it5.2
r_scangle_other5.199
r_mcangle_it4.814
r_mcangle_other4.814
r_scbond_it3.169
r_scbond_other3.163
r_mcbond_it3.055
r_mcbond_other3.053
r_angle_other_deg2.237
r_angle_refined_deg1.784
r_nbd_other0.229
r_symmetry_nbd_other0.196
r_symmetry_nbd_refined0.194
r_nbd_refined0.181
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_refined0.141
r_chiral_restr0.115
r_xyhbond_nbd_other0.084
r_symmetry_nbtor_other0.078
r_symmetry_xyhbond_nbd_other0.069
r_bond_other_d0.034
r_bond_refined_d0.014
r_gen_planes_other0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2925
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms83

Software

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