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Structure of full length unliganded CodY from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GX5 2GX5, 2B0L experimental model PDB 2B0L 2GX5, 2B0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 1.7M Li2SO4, sodium citrate pH 5.6, 3% dioxane
Crystal Properties Matthews coefficient Solvent content 3.1 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.524 α = 90 b = 111.524 β = 90 c = 119.536 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 4 2002-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.93300 ESRF BM14
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 3.7 25 97.5 0.059 33.14 6.1 8235
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 3.7 3.83 98.2 0.408 5.66 6.1
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 2GX5, 2B0L 3.71 24.94 7841 381 97 0.26905 0.26356 0.2623 0.38942 0.3807 RANDOM 83.452
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 77.221 r_sphericity_bonded 40.899 r_dihedral_angle_2_deg 40.502 r_dihedral_angle_3_deg 26.928 r_scbond_it 23.678 r_scbond_other 23.672 r_mcbond_it 22.974 r_mcbond_other 22.947 r_long_range_B_refined 20.789 r_long_range_B_other 20.789
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 77.221 r_sphericity_bonded 40.899 r_dihedral_angle_2_deg 40.502 r_dihedral_angle_3_deg 26.928 r_scbond_it 23.678 r_scbond_other 23.672 r_mcbond_it 22.974 r_mcbond_other 22.947 r_long_range_B_refined 20.789 r_long_range_B_other 20.789 r_scangle_other 20.667 r_mcangle_other 20.658 r_mcangle_it 20.656 r_dihedral_angle_4_deg 19.582 r_dihedral_angle_1_deg 9.172 r_angle_other_deg 3.421 r_angle_refined_deg 2.135 r_chiral_restr 0.134 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4004 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing