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Crystal structure of the thermostable Japanese Firefly Luciferase complexed with MgATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCI PDB ENTRY 1LCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 PEG4000, Lithium chrolide, ATP, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.78 α = 90 b = 181.975 β = 90 c = 53.566 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 293 IMAGE PLATE RIGAKU RAXIS IIC 1999-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.3 60 97.9 0.058 10.7 3.1 25394 25394 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) 2.3 2.38 91.1 0.15 4 2.55 2304
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LCI 2.3 60 25353 24062 1291 0.18151 0.18151 0.17898 0.1814 0.22766 0.1792 RANDOM 22.972
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 -0.18 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.703 r_scangle_it 2.932 r_scbond_it 1.714 r_angle_refined_deg 1.264 r_mcangle_it 1.151 r_mcbond_it 0.614 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.703 r_scangle_it 2.932 r_scbond_it 1.714 r_angle_refined_deg 1.264 r_mcangle_it 1.151 r_mcbond_it 0.614 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 3976 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing