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Crystal Structure of R134D mutant of YnaF (Universal Stress Protein F) from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R2L PDB ID 4R2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Under oil, Microbatch 8.5 298 30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 5mM Adenosine 5'-(beta,gamma-imido)triphosphate, Under oil, Microbatch, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.05 40.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.18 α = 90 b = 131.18 β = 90 c = 33 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 225 mm CCD bent collimating mirror and toroid 2014-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.978565 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.2 41.48 100 0.12 9.7 15273 32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.676 3.5 9.9 2167
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 PDB ID 4R2L 2.2 41.48 14470 765 99.97 0.19728 0.19532 0.2013 0.23435 0.2376 RANDOM 41.254
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] -0.29 -0.29 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.333 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_4_deg 8.72 r_dihedral_angle_1_deg 6.245 r_long_range_B_refined 5.629 r_long_range_B_other 5.555 r_scangle_other 2.617 r_mcangle_it 2.276 r_mcangle_other 2.276 r_angle_refined_deg 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.333 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_4_deg 8.72 r_dihedral_angle_1_deg 6.245 r_long_range_B_refined 5.629 r_long_range_B_other 5.555 r_scangle_other 2.617 r_mcangle_it 2.276 r_mcangle_other 2.276 r_angle_refined_deg 1.814 r_scbond_it 1.701 r_scbond_other 1.701 r_mcbond_it 1.412 r_mcbond_other 1.411 r_angle_other_deg 0.806 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2074 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 64
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling