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Crystal structure of HAD-like phosphatase yidA from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Experimental Phasing by single crystal SIRAS (Radiation damage).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG 3350, Magnesium Chloride,, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.12 α = 112.58 b = 54.871 β = 96.37 c = 67.725 γ = 106.79
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARRESEARCH 2003-08-06 M SINGLE WAVELENGTH 2 1 x-ray 120 CCD MARRESEARCH 2003-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 0.97901 NSLS X9A 2 SYNCHROTRON NSLS BEAMLINE X9A 1.0083 NSLS X9A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 24 95.9 0.043 0.064 30.9 3.7 106331 106331 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.45 93.4 0.37 0.56 2.58 10374
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Single Crystal SIRAS by RIP Throught Experimental Phasing by single crystal SIRAS (Radiation damage). 1.4 24.5 99828 99828 5253 95.5 0.185 0.177 0.1682 0.213 0.2036 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 22.2 p_staggered_tor 13.4 p_planar_tor 6.2 p_multtor_nbd 0.269 p_singtor_nbd 0.168 p_chiral_restr 0.139 p_xyhbond_nbd 0.105 p_planar_d 0.04 p_angle_d 0.034 p_plane_restr 0.031
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 22.2 p_staggered_tor 13.4 p_planar_tor 6.2 p_multtor_nbd 0.269 p_singtor_nbd 0.168 p_chiral_restr 0.139 p_xyhbond_nbd 0.105 p_planar_d 0.04 p_angle_d 0.034 p_plane_restr 0.031 p_bond_d 0.02 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4208 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELXE model building RESOLVE model building ARP/wARP model building REFMAC refinement RESOLVE phasing