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Structure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1 at medium resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V18 PDB ENTRY 4V18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.3 M AMMONIUM SULPHATE, 24% PEG 3350. CRYO 30% GLYCEROL IN ABOVE CONDITION, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.1 α = 90 b = 132.1 β = 90 c = 104.17 γ = 120
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 2013-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.59 50.14 99.9 0.12 15.5 18.2 10960
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 2.59 2.66 99.2 1.31 3.6 19.6
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 4V18 2.59 50.14 10433 526 99.63 0.22882 0.22745 0.2349 0.25843 0.2663 RANDOM 84.02
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] -3.61 -1.8 -3.61 11.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_1_deg 5.749 r_mcangle_it 1.478 r_angle_refined_deg 1.076 r_mcbond_it 0.83 r_mcbond_other 0.83 r_angle_other_deg 0.819 r_scbond_it 0.761 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_1_deg 5.749 r_mcangle_it 1.478 r_angle_refined_deg 1.076 r_mcbond_it 0.83 r_mcbond_other 0.83 r_angle_other_deg 0.819 r_scbond_it 0.761 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2264 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data scaling PHASER phasing