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Cwp2 from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 2.0 M amonium sulphate
0.1 M bis-tris
Crystal Properties Matthews coefficient Solvent content 4.23 70.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.828 α = 90 b = 134.828 β = 90 c = 102.835 γ = 120
Symmetry Space Group P 63 2 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 PIXEL DECTRIS PILATUS 6M 2015-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.9 120.83 100 0.021 1 21.6 62.5 43871
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.772 0.685 1.5 35.3
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 5J6Q 1.9 116.76 41879 1932 99.92 0.21637 0.21509 0.2234 0.24488 0.2513 RANDOM 41.762
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] -0.38 -0.19 -0.38 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.111 r_dihedral_angle_4_deg 14.621 r_dihedral_angle_3_deg 12.634 r_long_range_B_refined 8.252 r_long_range_B_other 7.718 r_dihedral_angle_1_deg 6.013 r_scangle_other 5.064 r_scbond_it 3.488 r_mcangle_it 3.442 r_mcangle_other 3.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.111 r_dihedral_angle_4_deg 14.621 r_dihedral_angle_3_deg 12.634 r_long_range_B_refined 8.252 r_long_range_B_other 7.718 r_dihedral_angle_1_deg 6.013 r_scangle_other 5.064 r_scbond_it 3.488 r_mcangle_it 3.442 r_mcangle_other 3.441 r_scbond_other 3.132 r_mcbond_it 2.344 r_mcbond_other 2.344 r_angle_refined_deg 1.44 r_angle_other_deg 0.886 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2196 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing