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1.78 Angstrom Resolution Crystal Structure of Hypothetical Protein CD630_05490 from Clostridioides difficile 630.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 Protein: 9.3 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME.
Crystal Properties Matthews coefficient Solvent content 1.19 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.62 α = 90 b = 58.688 β = 94.47 c = 77.329 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 MARMOSAIC 300 mm CCD C(111) 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.78 46.7 97.74 0.102 0.102 0.113 0.048 0.99 11.1 5.2 22345
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 97.89 0.83 0.83 0.95 0.45 0.61 2.1 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.78 24.52 21188 1127 97.68 0.24828 0.24634 0.2542 0.28386 0.2887 RANDOM 29.866
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] 1.12 0.42 -2.96 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.757 r_dihedral_angle_3_deg 10.112 r_long_range_B_refined 9.507 r_long_range_B_other 9.498 r_scangle_other 8.044 r_scbond_it 5.576 r_scbond_other 5.574 r_mcangle_it 5.177 r_mcangle_other 5.175 r_mcbond_it 3.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.757 r_dihedral_angle_3_deg 10.112 r_long_range_B_refined 9.507 r_long_range_B_other 9.498 r_scangle_other 8.044 r_scbond_it 5.576 r_scbond_other 5.574 r_mcangle_it 5.177 r_mcangle_other 5.175 r_mcbond_it 3.911 r_mcbond_other 3.907 r_dihedral_angle_1_deg 2.791 r_angle_refined_deg 1.456 r_angle_other_deg 0.396 r_chiral_restr 0.072 r_gen_planes_other 0.059 r_gen_planes_refined 0.057 r_bond_refined_d 0.008 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing