8OZV

Imine Reductase from Ajellomyces dermatitidis in complex with 2,2-difluoroacetophenone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G6R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.6298100 mM PO4 buffer pH 8.6; 0.2 M MgCl2; 20% (w/v) PEG 3350; 2M NADP+; 10 mM ligand
Crystal Properties
Matthews coefficientSolvent content
2.9458.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74α = 90
b = 74β = 90
c = 112.077γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS EIGER2 XE 9M2017-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.97950DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5242.221000.030.014152.1125531310.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.550.080.03124

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 REPLACEMENTTHROUGHOUT1.5242.2252466279999.990.132330.131530.14714RANDOM12.842
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]
0.230.120.23-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.472
r_dihedral_angle_2_deg6.831
r_dihedral_angle_1_deg5.965
r_long_range_B_refined5.693
r_long_range_B_other5.196
r_scangle_other3.866
r_scbond_it2.686
r_scbond_other2.685
r_mcangle_other2.034
r_mcangle_it2.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.472
r_dihedral_angle_2_deg6.831
r_dihedral_angle_1_deg5.965
r_long_range_B_refined5.693
r_long_range_B_other5.196
r_scangle_other3.866
r_scbond_it2.686
r_scbond_other2.685
r_mcangle_other2.034
r_mcangle_it2.029
r_angle_refined_deg1.974
r_mcbond_other1.366
r_mcbond_it1.365
r_angle_other_deg0.633
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms2090
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing