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Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1S PDB ENTRY 2D1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 293 PEG4000, Lithium chrolide, Magnesium chloride, HEPES, 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine, pH 7.8, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.468 α = 90 b = 181.174 β = 90 c = 52.239 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MAR CCD 165 mm 2002-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.00 SPring-8 BL44B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 25 97.6 0.09 6 6.9 94838 94838 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.53 95 0.283 1.9 7 13298
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2D1S 1.45 25 94802 90068 4734 0.16527 0.16527 0.16439 0.1676 0.18195 0.1654 RANDOM 11.89
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 -0.34 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.701 r_scangle_it 3.07 r_scbond_it 1.909 r_angle_refined_deg 1.381 r_mcangle_it 1.176 r_mcbond_it 0.651 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.701 r_scangle_it 3.07 r_scbond_it 1.909 r_angle_refined_deg 1.381 r_mcangle_it 1.176 r_mcbond_it 0.651 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.119 r_symmetry_hbond_refined 0.112 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 4126 Nucleic Acid Atoms Solvent Atoms 843 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling