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Crystal structure of glycosyl hydrolase family 5 (NP_809925.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.20M ammonium sulfate, 40.0% 2-methyl-2,4-pentanediol, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.335 α = 90 b = 261.335 β = 90 c = 183.87 γ = 120
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 mirror (vertical focusing) 2008-11-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162,0.97870,0.97814 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 85.176 100 0.124 11.7 6.4 139171 139171
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) 2.1 2.21 99.9 0.656 0.656 1.1 6.4 20050
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 2.1 85.176 139161 6991 99.99 0.187 0.185 0.1862 0.222 0.22 RANDOM 27.854
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.124 r_dihedral_angle_3_deg 9.459 r_dihedral_angle_4_deg 8.361 r_dihedral_angle_1_deg 3.197 r_scangle_it 2.392 r_scbond_it 1.631 r_mcangle_it 1.001 r_angle_refined_deg 0.843 r_angle_other_deg 0.629 r_mcbond_it 0.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.124 r_dihedral_angle_3_deg 9.459 r_dihedral_angle_4_deg 8.361 r_dihedral_angle_1_deg 3.197 r_scangle_it 2.392 r_scbond_it 1.631 r_mcangle_it 1.001 r_angle_refined_deg 0.843 r_angle_other_deg 0.629 r_mcbond_it 0.544 r_mcbond_other 0.121 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14947 Nucleic Acid Atoms Solvent Atoms 1208 Heterogen Atoms 160
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELX phasing SHARP phasing REFMAC refinement MolProbity model building PDB_EXTRACT data extraction SHELXD phasing autoSHARP phasing