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Crystal structure of RSL mutant in complex with sugar Ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 7.5 277 20 mM Tris-HCl, 100 mM of NaCl pH 7.5, Micro centrifuge tube sequentially put with RSL solution, pure buffer, ligand solution
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.494 α = 90 b = 161.519 β = 91.53 c = 54.137 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 CCD ADSC QUANTUM 315r 2019-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979183 SSRF BL17U1
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 1.61 80.76 98 0.079 0.086 0.034 0.998 15 6.3 94580
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 1.61 1.69 96.7 0.59 0.662 0.296 0.832 4.8
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 4csd 1.61 80.76 89341 4739 97.52 0.2194 0.2178 0.2257 0.2485 0.2534 RANDOM 21.416
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] -0.11 -0.09 0.05 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.151 r_dihedral_angle_3_deg 12.37 r_dihedral_angle_4_deg 10.543 r_dihedral_angle_1_deg 8.277 r_angle_refined_deg 1.96 r_angle_other_deg 1.585 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.151 r_dihedral_angle_3_deg 12.37 r_dihedral_angle_4_deg 10.543 r_dihedral_angle_1_deg 8.277 r_angle_refined_deg 1.96 r_angle_other_deg 1.585 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6087 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 420
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing