5XWV

Substrate-bound Structure of a Ketoreductase from the Second Module of the 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
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.319α = 73.09
b = 63.564β = 67.2
c = 71.886γ = 89.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97853SSRFBL19U1

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
11.85091.170.0659.81.976537
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)
11.81.8389.50.26521.8

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 REPLACEMENTTHROUGHOUT3MJE1.85076537416491.170.182070.18020.21726RANDOM23.71
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]
1.150.6-0.08-0.97-0.59-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg13.469
r_dihedral_angle_1_deg6.989
r_long_range_B_other6.35
r_long_range_B_refined6.347
r_scangle_other5.118
r_scbond_it3.502
r_scbond_other3.501
r_mcangle_it3.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg13.469
r_dihedral_angle_1_deg6.989
r_long_range_B_other6.35
r_long_range_B_refined6.347
r_scangle_other5.118
r_scbond_it3.502
r_scbond_other3.501
r_mcangle_it3.085
r_mcangle_other3.085
r_mcbond_it2.26
r_mcbond_other2.258
r_angle_refined_deg0.943
r_angle_other_deg0.556
r_chiral_restr0.058
r_gen_planes_refined0.018
r_bond_refined_d0.009
r_gen_planes_other0.002
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 Atoms6938
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms148

Software

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