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Crystal Structure of the Bacterial Luciferase:Flavin Complex Reveals the Basis of Intersubunit Communication
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.12 60.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.886 α = 90 b = 109.301 β = 90 c = 301.419 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 100 CCD MAR CCD 165 mm 2008-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 .9 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 27.33 99.9 0.429 0.096 43.3 11.1 83087 83194 26.842
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.36 99.08 0.204 0.287
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1LUC 2.3 27.33 83087 4385 99.87 0.18676 0.18672 0.1839 0.1849 0.24087 0.238 RANDOM 26.842
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.879 r_dihedral_angle_4_deg 22.295 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_1_deg 6.82 r_scangle_it 4.094 r_scbond_it 2.8 r_angle_refined_deg 1.681 r_mcangle_it 1.662 r_mcbond_it 1.084 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.879 r_dihedral_angle_4_deg 22.295 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_1_deg 6.82 r_scangle_it 4.094 r_scbond_it 2.8 r_angle_refined_deg 1.681 r_mcangle_it 1.662 r_mcbond_it 1.084 r_nbtor_refined 0.305 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.206 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 10927 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 121
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling