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Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 5.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.81 67.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.135 α = 90 b = 121.135 β = 90 c = 182.812 γ = 120
Symmetry Space Group P 63 2 2
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 2009-05-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97936,0.97919 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 1.8 29.988 100 0.101 0.101 14.3 7.3 73725 22.138
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 1.8 1.85 100 0.764 0.764 1 7.3 5333
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 1.8 29.988 73676 3714 99.96 0.151 0.15 0.1579 0.171 0.1802 RANDOM 29.571
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] 1.61 0.81 1.61 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.443 r_dihedral_angle_4_deg 22.615 r_dihedral_angle_3_deg 12.368 r_scangle_it 6.089 r_dihedral_angle_1_deg 5.038 r_scbond_it 4.819 r_mcangle_it 2.535 r_mcbond_it 1.988 r_angle_refined_deg 1.544 r_angle_other_deg 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.443 r_dihedral_angle_4_deg 22.615 r_dihedral_angle_3_deg 12.368 r_scangle_it 6.089 r_dihedral_angle_1_deg 5.038 r_scbond_it 4.819 r_mcangle_it 2.535 r_mcbond_it 1.988 r_angle_refined_deg 1.544 r_angle_other_deg 1.08 r_mcbond_other 0.549 r_symmetry_vdw_refined 0.241 r_symmetry_vdw_other 0.239 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.191 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.101 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3489 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHARP phasing