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Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 1.6000M (NH4)2SO4, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.93 57.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.729 α = 90 b = 69.729 β = 90 c = 124.569 γ = 120
Symmetry Space Group P 31 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 2009-05-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97936,0.97925 SSRL BL9-2
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 1.62 29.348 100 0.075 0.075 19.8 9.6 45318
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 1.62 1.66 99.6 0.684 0.684 2.2 7.4 3245
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.62 29.348 45270 2280 99.95 0.183 0.182 0.2041 0.201 0.2246 RANDOM 16.983
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] 0.21 0.11 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.126 r_dihedral_angle_4_deg 20.93 r_dihedral_angle_3_deg 14.961 r_dihedral_angle_1_deg 4.753 r_scangle_it 4.146 r_scbond_it 2.764 r_mcangle_it 1.601 r_angle_refined_deg 1.567 r_angle_other_deg 1.005 r_mcbond_it 0.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.126 r_dihedral_angle_4_deg 20.93 r_dihedral_angle_3_deg 14.961 r_dihedral_angle_1_deg 4.753 r_scangle_it 4.146 r_scbond_it 2.764 r_mcangle_it 1.601 r_angle_refined_deg 1.567 r_angle_other_deg 1.005 r_mcbond_it 0.935 r_mcbond_other 0.279 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1990 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing