5A9T

Imine Reductase from Amycolatopsis orientalis in complex with (R)- Methyltetrahydroisoquinoline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZGYPDB ENTRY 3ZGY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
190.2 M CALCIUM ACETATE, 0.1 M TRIS PH 9.0, 8% (W/V) PEG 550 MME, 8% (W/V) PEG 20K WITH PROTEIN AT A CONCENTRATION OF 20 MG PER ML
Crystal Properties
Matthews coefficientSolvent content
2.7655.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.999α = 90
b = 91.05β = 90
c = 90.976γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M2014-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.560.187.50.0422.46509652
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)
11.51.53570.432.83.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZGY1.560.147510250793.650.182560.18120.20828RANDOM21.571
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]
0.060.95-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.909
r_dihedral_angle_4_deg12.325
r_dihedral_angle_3_deg11.918
r_dihedral_angle_1_deg5.271
r_scbond_it3.535
r_mcangle_it2.747
r_angle_refined_deg2.451
r_mcbond_it2.021
r_mcbond_other2.006
r_angle_other_deg1.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.909
r_dihedral_angle_4_deg12.325
r_dihedral_angle_3_deg11.918
r_dihedral_angle_1_deg5.271
r_scbond_it3.535
r_mcangle_it2.747
r_angle_refined_deg2.451
r_mcbond_it2.021
r_mcbond_other2.006
r_angle_other_deg1.357
r_chiral_restr0.145
r_bond_refined_d0.027
r_gen_planes_refined0.013
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2079
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing