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Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP
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 8 293 PEG4000, Lithium chrolide, Magnesium chloride, ATP, D-Luciferin, Teis-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.612 α = 90 b = 181.402 β = 90 c = 52.743 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 RIGAKU JUPITER 210 2001-03-29 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 1.6 55 99.7 0.054 10.1 6.6 73719 73719 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) 1.6 1.66 97.4 0.21 3 3.6 7056
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2D1Q 1.6 55 73705 69987 3718 0.1854 0.1854 0.18409 0.21039 0.19 RANDOM 16.437
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] -0.16 -0.27 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.559 r_scangle_it 3.527 r_scbond_it 2.111 r_mcangle_it 1.351 r_angle_refined_deg 1.333 r_mcbond_it 0.726 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.559 r_scangle_it 3.527 r_scbond_it 2.111 r_mcangle_it 1.351 r_angle_refined_deg 1.333 r_mcbond_it 0.726 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 4111 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling