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Crystal structure of a red-emitter mutant of Lampyris turkestanicus luciferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BA3 PDB ENTRY 1BA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 4 % w/v PEG 8000, 14 % v/v Ethylenglycol, 100 mM Na-HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.009 α = 90 b = 85.009 β = 90 c = 97.097 γ = 90
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 RAYONIX MX-225 mirrors 2009-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2.13 32.37 99.7 0.133 12.27 38301 -3 27.756
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 2.13 2.19 97.2 0.644 2.5
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 (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 1BA3 2.13 31.98 38301 1915 99.6 0.1672 0.1651 0.1531 0.2076 0.1851 RANDOM 23.5514
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] 6.01 6.01 -12.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.881 r_dihedral_angle_4_deg 19.27 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 6.178 r_scangle_it 3.901 r_scbond_it 2.533 r_mcangle_it 1.628 r_angle_refined_deg 1.559 r_angle_other_deg 0.946 r_mcbond_it 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.881 r_dihedral_angle_4_deg 19.27 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 6.178 r_scangle_it 3.901 r_scbond_it 2.533 r_mcangle_it 1.628 r_angle_refined_deg 1.559 r_angle_other_deg 0.946 r_mcbond_it 0.92 r_mcbond_other 0.248 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3350 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 57
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction