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The X-ray crystal structure of a thermophilic cellobiose binding protein bound with cellobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VR5 pdb entry 1VR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.1M MES, 0.2M Ammonium Sulfate, 30% PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.03 α = 90 b = 107.03 β = 90 c = 118.19 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 MARMOSAIC 300 mm CCD 2006-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1.5 50 99.9 0.062 18.8 109675 109675 -3 22.909
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) 1.5 1.6 99.8 0.578 3 19013
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 1VR5 1.5 48.74 109673 109673 5484 100 0.193 0.193 0.192 0.216 0.22 RANDOM 13.423
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] -0.48 -0.48 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.585 r_dihedral_angle_4_deg 14.89 r_dihedral_angle_3_deg 11.419 r_dihedral_angle_1_deg 6.386 r_scangle_it 1.789 r_scbond_it 1.295 r_angle_refined_deg 1.12 r_mcangle_it 0.88 r_angle_other_deg 0.842 r_mcbond_it 0.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.585 r_dihedral_angle_4_deg 14.89 r_dihedral_angle_3_deg 11.419 r_dihedral_angle_1_deg 6.386 r_scangle_it 1.789 r_scbond_it 1.295 r_angle_refined_deg 1.12 r_mcangle_it 0.88 r_angle_other_deg 0.842 r_mcbond_it 0.602 r_symmetry_vdw_other 0.234 r_nbd_refined 0.2 r_nbd_other 0.186 r_nbtor_refined 0.184 r_symmetry_vdw_refined 0.177 r_mcbond_other 0.111 r_xyhbond_nbd_refined 0.103 r_symmetry_hbond_refined 0.085 r_nbtor_other 0.083 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4812 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 23
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction PHASER phasing