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Crystal structure of beta-glucosidase A from bacterium Clostridium cellulovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OD0 PDB ENTRY 1OD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1M Hepes, 21-23%(w/v) PEG 3350, 0.3-0.45M Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.498 α = 90 b = 128.498 β = 90 c = 264.06 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 315 Vertically Collimating Premirror, Toroidal Focusing Mirror 2008-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 1.9 30 99.2 0.062 27.5 6.7 172709 171402 1 31
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) 1.9 1.97 98 0.323 3.8 3.8 17061
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 PDB ENTRY 1OD0 1.9 28.3 151131 7980 92.04 0.14867 0.14606 0.1656 0.19832 0.2088 RANDOM 20.123
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] 1.69 1.69 -3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.031 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 12.089 r_sphericity_free 6.292 r_dihedral_angle_1_deg 4.698 r_scangle_it 4.635 r_sphericity_bonded 3.303 r_scbond_it 3.111 r_rigid_bond_restr 2.042 r_mcangle_it 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.031 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 12.089 r_sphericity_free 6.292 r_dihedral_angle_1_deg 4.698 r_scangle_it 4.635 r_sphericity_bonded 3.303 r_scbond_it 3.111 r_rigid_bond_restr 2.042 r_mcangle_it 2.01 r_angle_refined_deg 1.415 r_mcbond_it 1.259 r_chiral_restr 0.105 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14530 Nucleic Acid Atoms Solvent Atoms 2147 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing