5XWW

Substrate-bound Structure of G355T/Q364H mutant of a Ketoreductase from amphotericin Polyketide Synthases


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MJE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52933.4 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3648

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.066α = 72.67
b = 63.627β = 67.21
c = 71.586γ = 89.88
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.9778SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9662.4894.60.18.61.863286
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.961.9990.60.36821.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3MJE1.965060085320094.150.182140.18030.21656RANDOM31.437
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]
0.870.11-0.55-0.9-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.095
r_dihedral_angle_4_deg17.516
r_dihedral_angle_3_deg14.05
r_long_range_B_other8.213
r_long_range_B_refined8.21
r_dihedral_angle_1_deg6.731
r_scangle_other6.218
r_scbond_it4.104
r_scbond_other4.104
r_mcangle_it3.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.095
r_dihedral_angle_4_deg17.516
r_dihedral_angle_3_deg14.05
r_long_range_B_other8.213
r_long_range_B_refined8.21
r_dihedral_angle_1_deg6.731
r_scangle_other6.218
r_scbond_it4.104
r_scbond_other4.104
r_mcangle_it3.789
r_mcangle_other3.789
r_mcbond_it2.791
r_mcbond_other2.791
r_angle_refined_deg1.088
r_angle_other_deg0.58
r_chiral_restr0.062
r_gen_planes_refined0.016
r_bond_refined_d0.007
r_gen_planes_other0.003
r_bond_other_d
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 Atoms6946
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing