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The X-ray crystal structure of a thermophilic cellobiose binding protein bound with laminaripentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JSD PDB ENTRY 4JSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaripentaose was added to a final concentration of 1 mM prior to crystallization trials. Crystals were grown in drops containing 2 uL of the protein solution mixed with 2 uL of 0.2-0.3 M magnesium acetate or calcium acetate, 20-30% (wt/vol) PEG 3350 equilibrated against 900 uL of the same solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.922 α = 90 b = 89.785 β = 90 c = 108.321 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 293 IMAGE PLATE RIGAKU RAXIS IV++ 2012-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.07 50 95.9 0.052 0.037 16.6 4.3 33022 32940 2 2 34.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.13 98.5 0.494 0.368 3.5 4.2 2783
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 4JSD 2.07 48.075 1.34 33022 32940 1996 95.65 0.1894 0.1874 0.1909 0.2209 0.2207 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.465 f_angle_d 1.15 f_chiral_restr 0.066 f_plane_restr 0.009 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4780 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 57
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling