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Crystal structure of WCK4234 in complex with SME-1
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 0.2M lithium chloride, PEG 4000 20%
Crystal Properties Matthews coefficient Solvent content 1.94 36.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.374 α = 90 b = 51.484 β = 90.72 c = 129.687 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 2024-12-17 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) 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 2.8 29.15 99.8 0.112 0.987 7.4 7.7 11713
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 2.8 2.95 0.929
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 2.8 21.622 11694 538 99.625 0.239 0.2363 0.2361 0.3031 0.3024 4.964
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] -0.597 0.05 -1.155 1.75
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 49.19 r_mcangle_it 44.135 r_mcbond_it 34.96 r_dihedral_angle_3_deg 16.97 r_dihedral_angle_6_deg 13.457 r_dihedral_angle_2_deg 9.61 r_dihedral_angle_1_deg 7.563 r_rigid_bond_restr 5.873 r_scangle_it 1.533 r_angle_refined_deg 1.53
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 49.19 r_mcangle_it 44.135 r_mcbond_it 34.96 r_dihedral_angle_3_deg 16.97 r_dihedral_angle_6_deg 13.457 r_dihedral_angle_2_deg 9.61 r_dihedral_angle_1_deg 7.563 r_rigid_bond_restr 5.873 r_scangle_it 1.533 r_angle_refined_deg 1.53 r_scbond_it 0.778 r_symmetry_xyhbond_nbd_refined 0.31 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.303 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.22 r_chiral_restr 0.113 r_ncsr_local_group_1 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing