5OJL | pdb_00005ojl

Imine Reductase from Aspergillus terreus in complex with NADPH4 and dibenz[c,e]azepine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A9S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1 M Bis-tris pH 5.5. 25% w/v PEG 3350 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.329α = 90
b = 61.128β = 90
c = 167.811γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M-F2017-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.928190DiamondI04-1

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
11.5641.951000.040.02123.58.139537
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)
11.561.591000.750.410.882.38.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5A9S1.5641.9537441204399.970.237240.235080.250.27780.29RANDOM34.331
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]
-0.082.17-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_3_deg16.281
r_dihedral_angle_4_deg15.864
r_long_range_B_other6.699
r_long_range_B_refined6.698
r_dihedral_angle_1_deg6.348
r_scangle_other5.014
r_mcangle_it4.64
r_mcangle_other4.638
r_scbond_it3.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_3_deg16.281
r_dihedral_angle_4_deg15.864
r_long_range_B_other6.699
r_long_range_B_refined6.698
r_dihedral_angle_1_deg6.348
r_scangle_other5.014
r_mcangle_it4.64
r_mcangle_other4.638
r_scbond_it3.784
r_scbond_other3.774
r_mcbond_it3.598
r_mcbond_other3.594
r_angle_refined_deg2.173
r_angle_other_deg1.163
r_chiral_restr0.134
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2004
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing