2D1S

Crystal structure of the thermostable Japanese Firefly Luciferase complexed with High-energy intermediate analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D1QPDB ENTRY 2D1Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.8293PEG4000, Lithium chrolide, Magnesium chloride, HEPES, 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine, pH 7.8, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.586α = 90
b = 181.313β = 90
c = 52.038γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATERIGAKU RAXIS V2002-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.02SPring-8BL45XU

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
11.36099.20.0549413361113361111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3595.80.2092.63.712734

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2D1Q1.36013350412679467100.181150.181150.180110.2008RANDOM11.684
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]
-0.19-0.310.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.607
r_scangle_it2.795
r_scbond_it1.767
r_angle_refined_deg1.371
r_mcangle_it1.162
r_mcbond_it0.639
r_nbd_refined0.197
r_symmetry_vdw_refined0.166
r_chiral_restr0.12
r_xyhbond_nbd_refined0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.607
r_scangle_it2.795
r_scbond_it1.767
r_angle_refined_deg1.371
r_mcangle_it1.162
r_mcbond_it0.639
r_nbd_refined0.197
r_symmetry_vdw_refined0.166
r_chiral_restr0.12
r_xyhbond_nbd_refined0.098
r_symmetry_hbond_refined0.083
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4127
Nucleic Acid Atoms
Solvent Atoms794
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling