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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 7.5 291 0.1 M sodium citrate pH 5.6, 20 mM Tris-HCl pH 7.5, 35 % ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.34 63.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.869 α = 90 b = 110.55 β = 91.3 c = 257.414 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 4 mirror 2003-06-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.97820 SRS PX14.2
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 50 72 0.102 18.3 3.2 57358
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 0.51 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GX5, 2B0L 3 46.68 53946 2880 100 0.23279 0.23038 0.27936 0.2919 RANDOM 86.521
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 0.87 -0.31 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.97 r_dihedral_angle_3_deg 22.963 r_dihedral_angle_4_deg 19.872 r_dihedral_angle_1_deg 6.222 r_scangle_it 1.96 r_angle_refined_deg 1.607 r_scbond_it 1.313 r_mcangle_it 0.79 r_mcbond_it 0.615 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.97 r_dihedral_angle_3_deg 22.963 r_dihedral_angle_4_deg 19.872 r_dihedral_angle_1_deg 6.222 r_scangle_it 1.96 r_angle_refined_deg 1.607 r_scbond_it 1.313 r_mcangle_it 0.79 r_mcbond_it 0.615 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.309 r_nbd_refined 0.266 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20020 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing