2D1T

Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D1SPDB ENTRY 2D1S

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
2.2745.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.468α = 90
b = 181.174β = 90
c = 52.239γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMAR CCD 165 mm2002-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.00SPring-8BL44B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.452597.60.0966.9948389483811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.53950.2831.9713298

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 2D1S1.4525948029006847340.165270.165270.164390.18195RANDOM11.89
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]
-0.1-0.340.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.701
r_scangle_it3.07
r_scbond_it1.909
r_angle_refined_deg1.381
r_mcangle_it1.176
r_mcbond_it0.651
r_nbd_refined0.198
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.125
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.701
r_scangle_it3.07
r_scbond_it1.909
r_angle_refined_deg1.381
r_mcangle_it1.176
r_mcbond_it0.651
r_nbd_refined0.198
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.125
r_chiral_restr0.119
r_symmetry_hbond_refined0.112
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4126
Nucleic Acid Atoms
Solvent Atoms843
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling