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The Crystal Structure of a Protein in the Glycosyl Hydrolase Family 38 from Enterococcus faecalis to 2.55A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 0.4M NaH2PO4/1.6M K2HPO4, 0.1M Imidazole pH 8.0, 0.2M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.728 α = 90 b = 134.947 β = 90 c = 106.329 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315 2009-08-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-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 2.55 50 99.9 0.082 10.5 4.9 31505
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) 2.55 2.64 100 0.635 5
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 THROUGHOUT 2.55 42.04 31460 1590 99.8 0.225 0.222 0.2179 0.282 0.2783 RANDOM 54.99
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] 0.03 -0.1 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.602 r_dihedral_angle_3_deg 20.149 r_dihedral_angle_4_deg 17.159 r_dihedral_angle_1_deg 6.918 r_scangle_it 3.276 r_scbond_it 2.075 r_angle_refined_deg 1.387 r_mcangle_it 1.183 r_mcbond_it 0.602 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.602 r_dihedral_angle_3_deg 20.149 r_dihedral_angle_4_deg 17.159 r_dihedral_angle_1_deg 6.918 r_scangle_it 3.276 r_scbond_it 2.075 r_angle_refined_deg 1.387 r_mcangle_it 1.183 r_mcbond_it 0.602 r_chiral_restr 0.097 r_bond_refined_d 0.011 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 6425 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection SHELX phasing MLPHARE phasing DM phasing RESOLVE phasing Coot model building