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Crystal structure of CdiA-CT/CdiI complex from Y. kristensenii 33638
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 0.1 M MgCl2, 0.1 M Na citrate pH 5.0, 15% PEG4000, cryo 20% PEG400
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.89 α = 78.25 b = 57.146 β = 90.21 c = 64.302 γ = 79.11
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 Mirrors 2014-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
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 1.7 30 97.1 0.082 8.13 2.2 71046 -3
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 1.7 1.73 95.5 0.437 2.26 2.1
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 1.7 30 69621 1423 96.75 0.17448 0.17391 0.183 0.20222 0.2098 RANDOM 22.432
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] -0.19 0.97 0.44 1 0.08 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.578 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_1_deg 5.083 r_long_range_B_refined 5.079 r_long_range_B_other 4.965 r_scangle_other 2.327 r_mcangle_other 1.776 r_mcangle_it 1.775 r_scbond_it 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.578 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_1_deg 5.083 r_long_range_B_refined 5.079 r_long_range_B_other 4.965 r_scangle_other 2.327 r_mcangle_other 1.776 r_mcangle_it 1.775 r_scbond_it 1.486 r_scbond_other 1.486 r_angle_refined_deg 1.368 r_mcbond_it 1.044 r_mcbond_other 1.034 r_angle_other_deg 0.803 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 5015 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SBC-Collect data collection HKL-3000 data scaling HKL-3000 phasing HKL-3000 data reduction