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Crystal structure of beta-galactosidase C (BgaC) from Bacillus circulans ATCC 31382
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 10mg/ml Protein in 10mM Tris-HCl and 1mM EDTA (pH 7.5), Reservoir (20% (w/v) PEG 6000, 100mM HEPES, 0.2M NaCl, pH 7.0), Protein:Reservoir=1:1
, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.268 α = 90 b = 93.122 β = 125.67 c = 119.567 γ = 90
Symmetry Space Group C 1 2 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 BRUKER SMART 6500 2012-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 99.6 0.109 0.109 24.672 10.5 117585 -3
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 1.8 1.83 99.5 0.52 10.4 5888
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 3D3A 1.8 41.66 117416 5891 99.45 0.183 0.1829 0.1811 0.1925 0.2156 0.2255 RANDOM 22.489
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 -1.93 -0.71 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.448 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 8.677 r_scangle_it 6.285 r_scbond_it 4.201 r_mcangle_it 2.798 r_mcbond_it 1.805 r_angle_refined_deg 1.051 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.448 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 8.677 r_scangle_it 6.285 r_scbond_it 4.201 r_mcangle_it 2.798 r_mcbond_it 1.805 r_angle_refined_deg 1.051 r_chiral_restr 0.103 r_gen_planes_refined 0.019 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9435 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection