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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 5LOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 1M sodium citrate pH6.0, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 3.4 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 315.628 α = 90 b = 113.676 β = 113.23 c = 168.594 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 2001-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 0.98040 SRS PX14.1
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 4.5 20 71.4 0.09 6.77 3.9 29671
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 4.5 4.58 71.4 0.508 1.01 1.3
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 5LOJ 4.5 19.88 27647 1479 100 0.26008 0.25054 0.2518 0.42963 0.4151 RANDOM 235.091
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] -2 11.4 8.16 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.598 r_dihedral_angle_3_deg 23.427 r_dihedral_angle_4_deg 17.079 r_dihedral_angle_1_deg 8.202 r_scangle_it 4.361 r_mcangle_it 3.629 r_scbond_it 2.707 r_mcbond_it 2.071 r_angle_refined_deg 1.441 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.598 r_dihedral_angle_3_deg 23.427 r_dihedral_angle_4_deg 17.079 r_dihedral_angle_1_deg 8.202 r_scangle_it 4.361 r_mcangle_it 3.629 r_scbond_it 2.707 r_mcbond_it 2.071 r_angle_refined_deg 1.441 r_nbtor_refined 0.306 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.194 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 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 28154 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing