☰ Navigation Tabs
Crystal structure of the thermostable Japanese Firefly Luciferase complexed with High-energy intermediate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1Q PDB ENTRY 2D1Q
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 2.26 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.586 α = 90 b = 181.313 β = 90 c = 52.038 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 IMAGE PLATE RIGAKU RAXIS V 2002-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.02 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.3 60 99.2 0.054 9 4 133611 133611 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.35 95.8 0.209 2.6 3.7 12734
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 2D1Q 1.3 60 133504 126794 6710 0.18115 0.18115 0.18011 0.1826 0.2008 0.1797 RANDOM 11.684
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] -0.19 -0.31 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.607 r_scangle_it 2.795 r_scbond_it 1.767 r_angle_refined_deg 1.371 r_mcangle_it 1.162 r_mcbond_it 0.639 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.12 r_xyhbond_nbd_refined 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.607 r_scangle_it 2.795 r_scbond_it 1.767 r_angle_refined_deg 1.371 r_mcangle_it 1.162 r_mcbond_it 0.639 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.12 r_xyhbond_nbd_refined 0.098 r_symmetry_hbond_refined 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4127 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling