7R3D

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NADH, AND GLYCEROL (Absence of Nicotinamide ring)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RRM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5295.150.1M Bistris pH 5.5; 25% Polyethylene glycol 8000; 0.2M ammonium formate 9.25 mg/ml dissolved in 20mM Tris-HCl, pH7.5 that was supplemented with 0.5mM Fe and 10mM NADH and incubated for 10 min at room temperature.
Crystal Properties
Matthews coefficientSolvent content
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.96α = 90
b = 95.11β = 116.48
c = 69.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9999DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.448.53990.0380.99710.93.1214193316.97
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.42990.4050.8072.22.86

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1RRM1.448.53141898688398.9340.1580.15640.179418.664
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]
0.9140.0950.886-1.266
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.454
r_dihedral_angle_4_deg16.163
r_dihedral_angle_3_deg11.749
r_dihedral_angle_1_deg6.33
r_lrange_it3.687
r_lrange_other3.542
r_scangle_it2.62
r_scangle_other2.619
r_scbond_it1.697
r_scbond_other1.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.454
r_dihedral_angle_4_deg16.163
r_dihedral_angle_3_deg11.749
r_dihedral_angle_1_deg6.33
r_lrange_it3.687
r_lrange_other3.542
r_scangle_it2.62
r_scangle_other2.619
r_scbond_it1.697
r_scbond_other1.696
r_mcangle_it1.553
r_mcangle_other1.552
r_angle_other_deg1.459
r_angle_refined_deg1.398
r_mcbond_it1.029
r_mcbond_other1.028
r_nbd_refined0.216
r_symmetry_nbd_refined0.17
r_symmetry_nbd_other0.165
r_nbtor_refined0.162
r_nbd_other0.152
r_xyhbond_nbd_refined0.12
r_symmetry_xyhbond_nbd_refined0.116
r_symmetry_nbtor_other0.078
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5700
Nucleic Acid Atoms
Solvent Atoms595
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing