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High resolution structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V1K PDB ENTRY 4V1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1 M SODIUM CITRATE, 0.1 M MES PH 6.5, 30% GLYCEROL WAS ADDED IN ABOVE CONDITOIN FOR TEH CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 3.17 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.25 α = 90 b = 102.525 β = 90 c = 109.46 γ = 90
Symmetry Space Group I 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 ADSC QUANTUM 315r 2013-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.75 30.19 100 0.13 15.8 13.9 58166
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 1.75 1.84 100 1.38 1.8 11.3
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 4V1K 1.75 74.83 55267 2898 99.97 0.15956 0.15849 0.1692 0.17975 0.1876 RANDOM 26.966
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] 0.47 0.75 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.874 r_dihedral_angle_4_deg 36.663 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_1_deg 6.286 r_scbond_it 4.261 r_mcangle_it 2.859 r_mcbond_it 1.939 r_mcbond_other 1.937 r_angle_refined_deg 1.455 r_angle_other_deg 1.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.874 r_dihedral_angle_4_deg 36.663 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_1_deg 6.286 r_scbond_it 4.261 r_mcangle_it 2.859 r_mcbond_it 1.939 r_mcbond_other 1.937 r_angle_refined_deg 1.455 r_angle_other_deg 1.141 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 3042 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing