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Crystal Structure of SME-1 E166A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 4000, 0.2M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 2.22 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.708 α = 90 b = 51.828 β = 114.235 c = 77.192 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU HyPix-6000HE 2024-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.3 25.884 99.9 0.104 0.12 0.058 0.997 15.4 8.1 23268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.39 0.382 0.464 0.258 0.893 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 25.884 23254 1113 99.88 0.177 0.174 0.1755 0.2371 0.2383 22.98
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] -0.733 -0.745 -0.986 1.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.233 r_dihedral_angle_6_deg 14.076 r_dihedral_angle_2_deg 9.422 r_lrange_it 8.717 r_dihedral_angle_1_deg 6.646 r_scangle_it 3.405 r_mcangle_it 2.781 r_rigid_bond_restr 2.536 r_scbond_it 2.168 r_angle_refined_deg 1.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.233 r_dihedral_angle_6_deg 14.076 r_dihedral_angle_2_deg 9.422 r_lrange_it 8.717 r_dihedral_angle_1_deg 6.646 r_scangle_it 3.405 r_mcangle_it 2.781 r_rigid_bond_restr 2.536 r_scbond_it 2.168 r_angle_refined_deg 1.827 r_mcbond_it 1.677 r_symmetry_nbd_refined 0.318 r_nbtor_refined 0.304 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.137 r_symmetry_xyhbond_nbd_refined 0.122 r_ncsr_local_group_1 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4112 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing