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Characterization of a novel CBM from Clostridium perfringens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FRA PDB ENTRY 5FRA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.1M CH3COONA PH 4.5, 0.2M (CH3CHOO)2CA, 8% (PEG 550 MME AND PEG 20,000)
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.348 α = 90 b = 76.714 β = 93.46 c = 67.254 γ = 90
Symmetry Space Group P 1 21 1
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 315 2015-04-28 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 1.9 39.69 98.8 0.07 13.2 3.8 50882 2
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 1.9 1.94 93.4 0.39 3 3.5
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 5FRA 1.9 40.61 48349 2479 98.56 0.17471 0.17291 0.1747 0.20874 0.2104 RANDOM 18.228
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] 0.29 -0.51 -0.56 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.212 r_dihedral_angle_4_deg 19.257 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 7.387 r_scbond_it 2.224 r_mcangle_it 1.877 r_angle_refined_deg 1.718 r_mcbond_it 1.266 r_mcbond_other 1.245 r_angle_other_deg 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.212 r_dihedral_angle_4_deg 19.257 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 7.387 r_scbond_it 2.224 r_mcangle_it 1.877 r_angle_refined_deg 1.718 r_mcbond_it 1.266 r_mcbond_other 1.245 r_angle_other_deg 0.941 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4580 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing