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Structure of beta-hexosaminidase from Vibrio cholerae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 20% PEG 5000, 0.1M BisTris pH 6.5, 0.1M AmSulfate, 5% Glycerol; Cryo 30% Glycerol, 20% PEG 5000, 0.1M BisTris pH 6.5, 0.1M AmSulfate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.98 α = 90 b = 79.378 β = 90 c = 86.685 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 MARRESEARCH Vertical and Horizontal focusing mirrors 2004-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID .9790 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 1.8 20 100 0.15 11.07 8.7 31858 31858 -3 16.4
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) 1.8 1.86 100 0.283 8 3113
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.8 20 -3 31801 31801 1604 99.86 0.17182 0.17182 0.17015 0.1724 0.20314 0.2022 RANDOM 14.793
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] -0.52 1.13 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.008 r_dihedral_angle_4_deg 14.639 r_dihedral_angle_3_deg 12.693 r_dihedral_angle_1_deg 5.188 r_scangle_it 3.666 r_scbond_it 2.584 r_mcangle_it 1.264 r_angle_refined_deg 1.239 r_mcbond_it 1.219 r_angle_other_deg 0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.008 r_dihedral_angle_4_deg 14.639 r_dihedral_angle_3_deg 12.693 r_dihedral_angle_1_deg 5.188 r_scangle_it 3.666 r_scbond_it 2.584 r_mcangle_it 1.264 r_angle_refined_deg 1.239 r_mcbond_it 1.219 r_angle_other_deg 0.807 r_mcbond_other 0.204 r_nbd_refined 0.202 r_nbd_other 0.19 r_symmetry_vdw_other 0.184 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.122 r_nbtor_other 0.084 r_chiral_restr 0.08 r_xyhbond_nbd_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2559 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing