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cohesin and fibronectin type-III double module construct from the Clostridium perfringens glycoside hydrolase GH84C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4E PDB ENTRY 2O4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.28 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.245 α = 90 b = 48.644 β = 96.19 c = 36.9 γ = 90
Symmetry Space Group C 1 2 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 1.8 73.72 94 0.05 30.2 3.7 27684 1.9
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 1.8 1.85 94.5 0.5 1.9 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 2O4E 1.8 73.72 22089 1183 95.4 0.228 0.224 0.225 0.294 0.2929 RANDOM 29.93
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] -2.06 -0.78 2.5 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.745 r_dihedral_angle_4_deg 22.559 r_dihedral_angle_3_deg 15.446 r_dihedral_angle_1_deg 6.804 r_scangle_it 4.088 r_scbond_it 2.661 r_angle_refined_deg 1.732 r_mcangle_it 1.725 r_mcbond_it 1.052 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.745 r_dihedral_angle_4_deg 22.559 r_dihedral_angle_3_deg 15.446 r_dihedral_angle_1_deg 6.804 r_scangle_it 4.088 r_scbond_it 2.661 r_angle_refined_deg 1.732 r_mcangle_it 1.725 r_mcbond_it 1.052 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.204 r_symmetry_vdw_refined 0.2 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 1744 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHASER phasing