4M46

Crystal structure of a green-emitter native of Lampyris turkestanicus luciferase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277100 mM MES Sodium salt, 40% v/v PEG 400, 5% w/v PEG 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7354.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.1α = 90
b = 85.1β = 90
c = 96.63γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MDynamically bendable mirror2011-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9778SLSX10SA

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
12.796.6388.50.1673.3190481898434.6

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 1LCI2.796.63190481797697899.510.212320.212320.210420.24761RANDOM19.119
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]
0.470.47-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.619
r_dihedral_angle_3_deg13.638
r_dihedral_angle_4_deg12.428
r_dihedral_angle_1_deg4.107
r_angle_refined_deg0.825
r_scangle_it0.549
r_mcangle_it0.316
r_scbond_it0.311
r_mcbond_it0.171
r_chiral_restr0.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.619
r_dihedral_angle_3_deg13.638
r_dihedral_angle_4_deg12.428
r_dihedral_angle_1_deg4.107
r_angle_refined_deg0.825
r_scangle_it0.549
r_mcangle_it0.316
r_scbond_it0.311
r_mcbond_it0.171
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3339
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms

Software

Software
Software NamePurpose
HEIDIdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling