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Crystal Structure of a putative mutarotase (YeaD) from Salmonella typhimurium in monoclinic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HTA monomer of orthorhombic form of stYeaD (PDB code 2HTA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 300 15-25% PEG8K, 0.1M citrate pH 5.5, 0.2-0.5mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.553 α = 90 b = 47.599 β = 91.82 c = 138.086 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MARRESEARCH osmic mirrors 2005-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 30 0.99 0.085 16.4 22.22 50200 54.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 0.919 0.443 2.3 4503
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 monomer of orthorhombic form of stYeaD (PDB code 2HTA) 2.5 27.8 50310 47276 2480 99.12 0.19135 0.19135 0.18877 0.1864 0.23974 0.1942 RANDOM 32.472
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] 0.01 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.067 r_dihedral_angle_4_deg 23.896 r_dihedral_angle_3_deg 19.629 r_dihedral_angle_1_deg 8.602 r_scangle_it 5.548 r_scbond_it 3.986 r_angle_refined_deg 2.314 r_mcangle_it 2.174 r_mcbond_it 1.734 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.067 r_dihedral_angle_4_deg 23.896 r_dihedral_angle_3_deg 19.629 r_dihedral_angle_1_deg 8.602 r_scangle_it 5.548 r_scbond_it 3.986 r_angle_refined_deg 2.314 r_mcangle_it 2.174 r_mcbond_it 1.734 r_nbtor_refined 0.325 r_symmetry_vdw_refined 0.271 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.157 r_bond_refined_d 0.028 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9112 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing