5DAN

Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62890.2 M Calcium chloride dehydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20 % v/v 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
3.160.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.821α = 90
b = 84.821β = 90
c = 93.727γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
125095.80.19.81025576
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0398.43.39.6

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 REPLACEMENTTHROUGHOUT1PYF242.4124240128595.70.20630.20470.2369RANDOM35.755
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]
0.70.350.7-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.251
r_dihedral_angle_4_deg18.77
r_dihedral_angle_3_deg16.14
r_dihedral_angle_1_deg5.937
r_mcangle_it2.652
r_mcbond_it1.924
r_mcbond_other1.923
r_angle_refined_deg1.639
r_angle_other_deg1.027
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.251
r_dihedral_angle_4_deg18.77
r_dihedral_angle_3_deg16.14
r_dihedral_angle_1_deg5.937
r_mcangle_it2.652
r_mcbond_it1.924
r_mcbond_other1.923
r_angle_refined_deg1.639
r_angle_other_deg1.027
r_chiral_restr0.093
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2206
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing