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Crystal structure of a glycosyl hydrolases family 2 protein from Bacteroides thetaiotaomicron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BGA PDB entry 3BGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 50% PEG MME 2000, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.063 α = 90 b = 211.075 β = 90 c = 71.085 γ = 90
Symmetry Space Group P 21 21 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 MAR CCD 165 mm 2008-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97900 APS 31-ID
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 2.8 47 96 0.146 16 10 29182 29182
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) 2.8 2.95 88 0.436 5.4 9.3 3846
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BGA 2.8 20 27576 27576 1491 95.55 0.1871 0.18406 0.24312 0.2106 RANDOM 30.746
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] 0.2 -0.73 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.519 r_dihedral_angle_4_deg 18.504 r_dihedral_angle_3_deg 17.972 r_dihedral_angle_1_deg 6.738 r_scangle_it 3.236 r_scbond_it 1.995 r_angle_refined_deg 1.511 r_mcangle_it 1.249 r_mcbond_it 0.633 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.519 r_dihedral_angle_4_deg 18.504 r_dihedral_angle_3_deg 17.972 r_dihedral_angle_1_deg 6.738 r_scangle_it 3.236 r_scbond_it 1.995 r_angle_refined_deg 1.511 r_mcangle_it 1.249 r_mcbond_it 0.633 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7949 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling MOLREP phasing