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Crystal structure of a glycoside hydrolase in complex with cellobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 MgCl2, Tris-Cl, PEG4000
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.337 α = 90 b = 54.315 β = 90 c = 84.848 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2016-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.36 25 99.9 0.035 27.2 10.8 46675
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.41 99.7 0.104 0.996 10.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OA7 1.36 25 44309 2302 99.76 0.1426 0.1414 0.1643 0.1861 RANDOM 15.275
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] 0.09 -0.06 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.768 r_dihedral_angle_4_deg 11.651 r_dihedral_angle_3_deg 9.97 r_dihedral_angle_1_deg 7.303 r_mcangle_it 2.098 r_angle_refined_deg 1.602 r_mcbond_it 1.527 r_mcbond_other 1.518 r_angle_other_deg 0.843 r_chiral_restr 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.768 r_dihedral_angle_4_deg 11.651 r_dihedral_angle_3_deg 9.97 r_dihedral_angle_1_deg 7.303 r_mcangle_it 2.098 r_angle_refined_deg 1.602 r_mcbond_it 1.527 r_mcbond_other 1.518 r_angle_other_deg 0.843 r_chiral_restr 0.313 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1562 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing