2D1Q

Crystal structure of the thermostable Japanese Firefly Luciferase complexed with MgATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LCIPDB ENTRY 1LCI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5293PEG4000, Lithium chrolide, ATP, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3547.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.78α = 90
b = 181.975β = 90
c = 53.566γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IIC1999-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.36097.90.05810.73.1253942539411
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)
2.32.3891.10.1542.552304

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LCI2.360253532406212910.181510.181510.178980.22766RANDOM22.972
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]
-1.64-0.181.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.703
r_scangle_it2.932
r_scbond_it1.714
r_angle_refined_deg1.264
r_mcangle_it1.151
r_mcbond_it0.614
r_symmetry_vdw_refined0.194
r_nbd_refined0.193
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.703
r_scangle_it2.932
r_scbond_it1.714
r_angle_refined_deg1.264
r_mcangle_it1.151
r_mcbond_it0.614
r_symmetry_vdw_refined0.194
r_nbd_refined0.193
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.134
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms3976
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing