2D1R

Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8293PEG4000, Lithium chrolide, Magnesium chloride, ATP, D-Luciferin, Teis-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.612α = 90
b = 181.402β = 90
c = 52.743γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDRIGAKU JUPITER 2102001-03-29MSINGLE 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
11.65599.70.05410.16.6737197371911
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)
1.61.6697.40.2133.67056

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 2D1Q1.655737056998737180.18540.18540.184090.21039RANDOM16.437
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]
-0.16-0.270.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.559
r_scangle_it3.527
r_scbond_it2.111
r_mcangle_it1.351
r_angle_refined_deg1.333
r_mcbond_it0.726
r_nbd_refined0.196
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.107
r_symmetry_hbond_refined0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.559
r_scangle_it3.527
r_scbond_it2.111
r_mcangle_it1.351
r_angle_refined_deg1.333
r_mcbond_it0.726
r_nbd_refined0.196
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.107
r_symmetry_hbond_refined0.102
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms4111
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling