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Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 EBS INTERNAL TRACKING NUMBER 234629B12. : BUCEA.18451.A PW36254 AT 20 MG/ML IN 25 MM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL x 0.4 uL drop with MORPHEUS SCREEN B12: 90 mM Halogens (NaF, NaBr, NaI, 0.1 M Tris/Bicine pH 8.5, 37.5% MPD-PEG1000-PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.98 37.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.83 α = 90 b = 89.68 β = 91.07 c = 67.1 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2012-05-31 M SINGLE WAVELENGTH 2 1 100 CCD RIGAKU SATURN 944+ 2012-05-25
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.03317 SSRL BL7-1 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 1.38 99.7 99.7 0.047 22.51 118123 -3 18.888
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 1.38 1.42 99.9 0.492 3.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1.38 99.7 118094 5916 0.157 0.155 0.1551 0.188 0.1882 RANDOM 15.9542
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] -0.26 0.1 0.98 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_sphericity_free 15.643 r_dihedral_angle_4_deg 15.257 r_dihedral_angle_3_deg 12.778 r_sphericity_bonded 8.671 r_dihedral_angle_1_deg 5.667 r_rigid_bond_restr 2.138 r_angle_refined_deg 1.324 r_chiral_restr 0.08 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_sphericity_free 15.643 r_dihedral_angle_4_deg 15.257 r_dihedral_angle_3_deg 12.778 r_sphericity_bonded 8.671 r_dihedral_angle_1_deg 5.667 r_rigid_bond_restr 2.138 r_angle_refined_deg 1.324 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4911 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction