8CP2

Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and L-aspartate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52939% PEG 4000, 1.2 M di-Na tartrate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 244.591α = 90
b = 244.591β = 90
c = 128.114γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87313ESRFID23-2

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
12.1122.31000.1860.3010.0930.9937.410.6166781
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141001.82.4390.7360.47310.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1122.3158494826799.970.180450.179310.20207RANDOM33.891
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]
-0.72-0.36-0.722.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.992
r_dihedral_angle_4_deg20.944
r_dihedral_angle_3_deg14.71
r_long_range_B_refined8.425
r_long_range_B_other8.425
r_dihedral_angle_1_deg7.092
r_scangle_other6.912
r_scbond_it4.731
r_scbond_other4.73
r_mcangle_it4.457
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.992
r_dihedral_angle_4_deg20.944
r_dihedral_angle_3_deg14.71
r_long_range_B_refined8.425
r_long_range_B_other8.425
r_dihedral_angle_1_deg7.092
r_scangle_other6.912
r_scbond_it4.731
r_scbond_other4.73
r_mcangle_it4.457
r_mcangle_other4.457
r_mcbond_it3.133
r_mcbond_other3.13
r_angle_refined_deg1.97
r_angle_other_deg1.384
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9279
Nucleic Acid Atoms
Solvent Atoms796
Heterogen Atoms285

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing