5NNO

Structure of TbALDH3 complexed with NAD and AN3057 aldehyde


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293.15100 mM Bis-Tris pH 5.5, 0.2 M LiSO4, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.168α = 90
b = 62.524β = 100.08
c = 92.974γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.546.5697.60.0740.98912.93.1343067.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.693.90.1120.96882.6

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 REPLACEMENTTHROUGHOUT5MYP2.546.5632560173685.880.236130.233890.27807RANDOM26.145
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]
-7.85-4.06-13.2221.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.399
r_dihedral_angle_3_deg15.188
r_dihedral_angle_4_deg14.981
r_dihedral_angle_1_deg6.651
r_long_range_B_refined1.967
r_long_range_B_other1.954
r_angle_refined_deg1.551
r_angle_other_deg0.991
r_scangle_other0.346
r_scbond_it0.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.399
r_dihedral_angle_3_deg15.188
r_dihedral_angle_4_deg14.981
r_dihedral_angle_1_deg6.651
r_long_range_B_refined1.967
r_long_range_B_other1.954
r_angle_refined_deg1.551
r_angle_other_deg0.991
r_scangle_other0.346
r_scbond_it0.241
r_scbond_other0.241
r_chiral_restr0.082
r_mcbond_other0.041
r_mcbond_it0.04
r_mcangle_other0.016
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
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_mcangle_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7512
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing