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Crystal structure of BT1871 retaining glycosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 100mM MES/NaOH buffer, 12% PEG 6000, 10% PEG 10000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.4 63.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.962 α = 90 b = 167.1 β = 90 c = 192.182 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 50 100 0.087 87930 23.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 99.7 0.365 8714
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2D73 2.3 19.94 2 86339 6159 98.4 0.186 0.186 0.187 0.218 0.1866 RANDOM 30
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] 15.03 -10.91 -4.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 2.79 c_scbond_it 1.98 c_mcangle_it 1.68 c_angle_deg 1.4 c_mcbond_it 1.09 c_improper_angle_d 0.81 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 2.79 c_scbond_it 1.98 c_mcangle_it 1.68 c_angle_deg 1.4 c_mcbond_it 1.09 c_improper_angle_d 0.81 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10216 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 14
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing