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Crystal Structure of a putative mutarotase (YeaD) from Salmonella typhimurium in orthorhombic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JOV PDB ENTRY 1JOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 300 1.5- 2M ammonium sulfate, 25mM magnesium formate, 0.1M Na cacodylate pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.751 α = 90 b = 88.774 β = 90 c = 179.294 γ = 90
Symmetry Space Group P 21 21 21
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 MAC Science DIP-2040 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.9 50 0.959 0.075 22.4 14.2 63880 24.2
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) 1 1.9 1.97 0.938 0.137 4.3 5886
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 PDB ENTRY 1JOV 1.9 39.07 61215 58059 3098 95.74 0.18704 0.18704 0.18512 0.1855 0.22258 0.2214 RANDOM 26.213
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 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.929 r_dihedral_angle_4_deg 21.778 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 7.553 r_scangle_it 4.355 r_scbond_it 2.96 r_mcangle_it 1.772 r_angle_refined_deg 1.705 r_mcbond_it 1.527 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.929 r_dihedral_angle_4_deg 21.778 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 7.553 r_scangle_it 4.355 r_scbond_it 2.96 r_mcangle_it 1.772 r_angle_refined_deg 1.705 r_mcbond_it 1.527 r_nbtor_refined 0.309 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4550 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing