5MIQ

Crystal Structure of Lactococcus lactis Thioredoxin Reductase Exposed to Visible Light (60 min)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F6M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29235% PEG 1500, 400 mM Li2SO4, 20 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
3.3563.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.46α = 90
b = 121.46β = 90
c = 60.71γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.97898MAX III911-3

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
11.9242.9599.60.0960.99915.697.435159
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)
11.921.9799.81.4610.4951.186.3

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 REPLACEMENTTHROUGHOUT1F6M1.9242.9433363175899.680.19640.19470.2276RANDOM35.457
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]
0.430.43-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.431
r_dihedral_angle_4_deg22.476
r_dihedral_angle_3_deg15.592
r_dihedral_angle_1_deg7.411
r_mcangle_it4.193
r_mcbond_it3.198
r_mcbond_other3.198
r_angle_refined_deg2.033
r_angle_other_deg0.874
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.431
r_dihedral_angle_4_deg22.476
r_dihedral_angle_3_deg15.592
r_dihedral_angle_1_deg7.411
r_mcangle_it4.193
r_mcbond_it3.198
r_mcbond_other3.198
r_angle_refined_deg2.033
r_angle_other_deg0.874
r_chiral_restr0.122
r_bond_refined_d0.019
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 Atoms2347
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing