6IAU

Amine Dehydrogenase from Cystobacter fuscus in complex with NADP+ and cyclohexylamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GET 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52982.0 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5; 10 mM NADP+; 20 mM cyclohexylamine
Crystal Properties
Matthews coefficientSolvent content
2.1443

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51α = 90
b = 87β = 90
c = 143γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS3 S 6M2018-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

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
11.9755.241000.130.0819.27.74590119
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)
11.972.020.750.430.852.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6GET1.9755.2443558226599.950.191440.190080.21734RANDOM25.738
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]
-1.764.12-2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.305
r_dihedral_angle_4_deg17.105
r_dihedral_angle_3_deg15.15
r_dihedral_angle_1_deg7.168
r_long_range_B_refined5.365
r_long_range_B_other5.334
r_scangle_other3.981
r_mcangle_it3.207
r_mcangle_other3.207
r_scbond_it2.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.305
r_dihedral_angle_4_deg17.105
r_dihedral_angle_3_deg15.15
r_dihedral_angle_1_deg7.168
r_long_range_B_refined5.365
r_long_range_B_other5.334
r_scangle_other3.981
r_mcangle_it3.207
r_mcangle_other3.207
r_scbond_it2.712
r_scbond_other2.712
r_mcbond_it2.213
r_mcbond_other2.212
r_angle_refined_deg1.684
r_angle_other_deg1.452
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5055
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing