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Crystal structure of H119A mutant of YdaA (Universal Stress Protein E) from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R2J PDB ID 4R2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Under oil, Microbatch 298 2M Ammonium sulfate, Under oil, Microbatch, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.82 α = 90 b = 79.82 β = 90 c = 262.95 γ = 120
Symmetry Space Group P 65 2 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 2012-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.953725 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 1.97 39.91 100 0.086 14.6 36482
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 1.97 2.07 100 0.348 7.3 14.3
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 4R2J 1.97 39.46 34480 1811 99.72 0.18969 0.1876 0.1959 0.22857 0.2389 RANDOM 27.83
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] 0.87 0.43 0.87 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.682 r_dihedral_angle_4_deg 19.04 r_dihedral_angle_3_deg 13.347 r_long_range_B_refined 7.122 r_long_range_B_other 7.122 r_dihedral_angle_1_deg 6.038 r_scangle_other 3.49 r_scbond_it 2.48 r_scbond_other 2.403 r_mcangle_other 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.682 r_dihedral_angle_4_deg 19.04 r_dihedral_angle_3_deg 13.347 r_long_range_B_refined 7.122 r_long_range_B_other 7.122 r_dihedral_angle_1_deg 6.038 r_scangle_other 3.49 r_scbond_it 2.48 r_scbond_other 2.403 r_mcangle_other 1.956 r_mcangle_it 1.953 r_angle_refined_deg 1.857 r_mcbond_it 1.34 r_mcbond_other 1.34 r_angle_other_deg 0.893 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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 2438 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 105
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling