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Crystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Na-cacodylate, PEG 8000, calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.44 49.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.08 α = 90 b = 72.354 β = 108.14 c = 78.381 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 PIXEL DECTRIS PILATUS 6M 2019-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.9 50 98.6 0.964 12.1 5.5 35911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 0.73
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 1.9 49.06 34073 1838 98.31 0.15614 0.1544 0.1688 0.18783 0.1986 RANDOM 15.915
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] 0.8 -0.93 -0.64 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.746 r_dihedral_angle_2_deg 7.516 r_dihedral_angle_1_deg 6.493 r_long_range_B_refined 6.264 r_long_range_B_other 5.842 r_scangle_other 3.618 r_mcangle_other 2.486 r_mcangle_it 2.484 r_scbond_it 2.265 r_scbond_other 2.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.746 r_dihedral_angle_2_deg 7.516 r_dihedral_angle_1_deg 6.493 r_long_range_B_refined 6.264 r_long_range_B_other 5.842 r_scangle_other 3.618 r_mcangle_other 2.486 r_mcangle_it 2.484 r_scbond_it 2.265 r_scbond_other 2.264 r_mcbond_it 1.586 r_mcbond_other 1.584 r_angle_refined_deg 1.509 r_angle_other_deg 0.552 r_chiral_restr 0.249 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3270 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing