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Crystal Structure of SME-1 with improved electron density
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 2.16 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.011 α = 90 b = 51.918 β = 113.25 c = 74.925 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 2024-06-24 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) 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 2.57 24.301 99.9 0.995 12.2 12.2 16226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.68 0.854
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 2.57 24.301 16216 767 99.84 0.208 0.2048 0.2051 0.2803 0.2804 17.462
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] 1.235 -0.58 -0.885 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.425 r_dihedral_angle_6_deg 12.902 r_dihedral_angle_1_deg 7.129 r_dihedral_angle_2_deg 6.526 r_lrange_it 6.124 r_rigid_bond_restr 3.804 r_scangle_it 2.566 r_mcangle_it 2.269 r_angle_refined_deg 1.842 r_scbond_it 1.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.425 r_dihedral_angle_6_deg 12.902 r_dihedral_angle_1_deg 7.129 r_dihedral_angle_2_deg 6.526 r_lrange_it 6.124 r_rigid_bond_restr 3.804 r_scangle_it 2.566 r_mcangle_it 2.269 r_angle_refined_deg 1.842 r_scbond_it 1.591 r_mcbond_it 1.365 r_symmetry_nbd_refined 0.326 r_nbtor_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.28 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.137 r_ncsr_local_group_1 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing