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Crystal structure of streptococcal beta-galactosidase in complex with galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E8D
Crystallization Crystal Properties Matthews coefficient Solvent content 2.29 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.351 α = 90 b = 82.374 β = 106.84 c = 99.596 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 MARMOSAIC 225 mm CCD 2011-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 50 96.8 91359 88435 -3 25.04
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 1.95 2.02 96.8 0.062 0.062 13.3 2.4 88435
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4E8D 1.95 50 87941 4395 96.98 0.2068 0.2049 0.2158 0.243 0.2459 RANDOM 40.5586
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] -4.85 -1.83 7.39 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.875 r_dihedral_angle_4_deg 18.255 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 5.56 r_scangle_it 4.575 r_mcangle_it 3.928 r_scbond_it 3.344 r_mcbond_it 2.985 r_angle_refined_deg 0.941 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.875 r_dihedral_angle_4_deg 18.255 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 5.56 r_scangle_it 4.575 r_mcangle_it 3.928 r_scbond_it 3.344 r_mcbond_it 2.985 r_angle_refined_deg 0.941 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9688 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 114
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling