7QZL

Amine Dehydrogenase from Cystobacter fuscus (CfusAmDH) W145A mutant with NADP+ and pentylamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M bis-Tris pH 5.5; 25% PEG 3350 10 mM NADP, 10 mM n-pentylamine
Crystal Properties
Matthews coefficientSolvent content
2.2845.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.691α = 90
b = 84.31β = 90
c = 284.13γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS EIGER2 XE 16M2021-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976284DiamondI03

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
11.547.41000.080.04117.112.210930617
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)
11.51.530.960.40.93.1

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 REPLACEMENTTHROUGHOUT6IAU1.547.4103793541799.980.16560.16440.1889RANDOM20.362
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]
0.930.96-1.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.971
r_dihedral_angle_4_deg17.732
r_dihedral_angle_3_deg11.903
r_dihedral_angle_1_deg6.729
r_angle_refined_deg1.742
r_angle_other_deg1.552
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.971
r_dihedral_angle_4_deg17.732
r_dihedral_angle_3_deg11.903
r_dihedral_angle_1_deg6.729
r_angle_refined_deg1.742
r_angle_other_deg1.552
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5148
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing