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Crystal Structure of Nanoluc Luciferase Mutant R164Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 Protein: 0.2 ul of 9 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP.
Precipitant: 0.2uL 0.2M Na nitrate, 20%w/v PEG 3350 (MCSG Suite 2 #34).
Cryo-protection: air-drying (slow dehydration)
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.18 α = 90 b = 62.045 β = 90 c = 97.304 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 50 99.9 0.038 0.042 0.017 0.996 11.6 5.7 40852 -3 12.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 1.114 1.114 1.221 0.496 0.682 1.7 5.9
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 5IBO 1.7 39.51 35957 1837 92.5 0.1739 0.1726 0.1838 0.1995 0.2078 RANDOM 30.486
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] 0.05 -0.32 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.094 r_dihedral_angle_4_deg 20.235 r_dihedral_angle_3_deg 12.399 r_dihedral_angle_1_deg 7.042 r_angle_other_deg 1.36 r_angle_refined_deg 1.352 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.094 r_dihedral_angle_4_deg 20.235 r_dihedral_angle_3_deg 12.399 r_dihedral_angle_1_deg 7.042 r_angle_other_deg 1.36 r_angle_refined_deg 1.352 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2628 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 43
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing