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Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 NANODROP, 15.0% PEG 8000, 8.0% Ethylene glycol, 0.1M Bicine pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.436 α = 90 b = 137.504 β = 90 c = 279.051 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 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97925, 0.97939, 0.94926 APS 23-ID-D
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 2.2 49.029 98.3 0.164 5.73 224828 -3 34.1
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 2.2 2.43 89.3 0.806 1.6
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 2.2 49.029 221971 11153 98.75 0.21 0.207 0.2122 0.252 0.2539 RANDOM 26.737
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] 1.32 -1.03 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_4_deg 18.2 r_dihedral_angle_3_deg 15.206 r_scangle_it 6.276 r_dihedral_angle_1_deg 5.647 r_scbond_it 4.784 r_mcangle_it 2.673 r_mcbond_it 1.686 r_angle_refined_deg 1.416 r_angle_other_deg 0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_4_deg 18.2 r_dihedral_angle_3_deg 15.206 r_scangle_it 6.276 r_dihedral_angle_1_deg 5.647 r_scbond_it 4.784 r_mcangle_it 2.673 r_mcbond_it 1.686 r_angle_refined_deg 1.416 r_angle_other_deg 0.958 r_mcbond_other 0.383 r_nbd_refined 0.219 r_nbd_other 0.196 r_symmetry_vdw_other 0.193 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.142 r_nbtor_other 0.088 r_chiral_restr 0.082 r_xyhbond_nbd_other 0.07 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25568 Nucleic Acid Atoms Solvent Atoms 1624 Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing