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Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2000M calcium chloride, 28.0000% polyethylene glycol 400, 0.1M HEPES pH 7.5, 0.005M 2'-deoxyadenosine 5'-monophosphate (dAMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.243 α = 90 b = 121.866 β = 121.36 c = 66.621 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-03-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97939,0.97925 SSRL BL9-2
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 1.98 48.741 99.4 0.053 15.73 47810 -3 29.174
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) 1.98 2.05 99.5 0.504 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.98 48.741 47810 2418 99.74 0.167 0.166 0.2 0.1914 RANDOM 36.888
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] 1.08 -0.41 -0.86 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_4_deg 16.054 r_dihedral_angle_3_deg 13.609 r_scangle_it 6.413 r_scbond_it 4.491 r_dihedral_angle_1_deg 4.421 r_mcangle_it 2.79 r_mcbond_it 1.62 r_angle_refined_deg 1.401 r_angle_other_deg 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_4_deg 16.054 r_dihedral_angle_3_deg 13.609 r_scangle_it 6.413 r_scbond_it 4.491 r_dihedral_angle_1_deg 4.421 r_mcangle_it 2.79 r_mcbond_it 1.62 r_angle_refined_deg 1.401 r_angle_other_deg 0.956 r_mcbond_other 0.716 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4965 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing