7NM8

The crystal structure of the antimycin pathway standalone ketoreductase, AntM, in complex with NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OSP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298.150.1 M Tris, pH 8.5, 5% w/v PEG 8K, 20% v/v PEG 300, 10% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3347.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.223α = 90
b = 92.223β = 90
c = 113.751γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.765.36100124.721.233683
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.730.958

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 REPLACEMENTTHROUGHOUT4osp1.765.3632045163899.9530.20.19870.224238.772
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]
1.670.8351.67-5.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.557
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg12.985
r_dihedral_angle_1_deg6.577
r_lrange_other6.236
r_lrange_it6.234
r_scangle_it5.292
r_scangle_other5.29
r_mcangle_it4.077
r_mcangle_other4.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.557
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg12.985
r_dihedral_angle_1_deg6.577
r_lrange_other6.236
r_lrange_it6.234
r_scangle_it5.292
r_scangle_other5.29
r_mcangle_it4.077
r_mcangle_other4.068
r_scbond_it3.78
r_scbond_other3.778
r_mcbond_it3.305
r_mcbond_other3.291
r_angle_other_deg2.414
r_angle_refined_deg1.657
r_symmetry_nbd_other0.222
r_nbd_other0.221
r_nbd_refined0.218
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.15
r_symmetry_xyhbond_nbd_refined0.124
r_symmetry_xyhbond_nbd_other0.123
r_symmetry_nbd_refined0.107
r_chiral_restr0.08
r_symmetry_nbtor_other0.069
r_bond_other_d0.036
r_gen_planes_other0.013
r_bond_refined_d0.01
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1810
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing