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Crystal structure of Catabolite repressor acivator from E. coli in complex with HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 HEPES, MgCl2, PEG 4000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.33 α = 90 b = 108.9 β = 90 c = 123.93 γ = 90
Symmetry Space Group P 2 21 21
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 300K 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.89 108.9 90.1 0.046 0.046 0.997 12.5 1.8 12352
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3.06 0.341 0.341 0.883
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 MOLECULAR REPLACEMENT THROUGHOUT 2.89 54.51 11741 590 89.48 0.22678 0.22398 0.2271 0.2827 0.2844 RANDOM 70
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] 1.58 0.72 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.352 r_dihedral_angle_1_deg 6.284 r_dihedral_angle_2_deg 4.751 r_long_range_B_refined 3.858 r_long_range_B_other 3.858 r_mcangle_it 2.142 r_mcangle_other 2.142 r_scangle_other 1.791 r_mcbond_it 1.195 r_mcbond_other 1.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.352 r_dihedral_angle_1_deg 6.284 r_dihedral_angle_2_deg 4.751 r_long_range_B_refined 3.858 r_long_range_B_other 3.858 r_mcangle_it 2.142 r_mcangle_other 2.142 r_scangle_other 1.791 r_mcbond_it 1.195 r_mcbond_other 1.195 r_scbond_it 0.957 r_scbond_other 0.957 r_angle_refined_deg 0.746 r_angle_other_deg 0.27 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 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 4440 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing