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Structure of the citrate-bound extracytoplasmic PAS domain of histidine kinase CitA from Geobacillus thermodenitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J80 2J80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 1 M tri-sodium citrate, pH 9.0, 0.1 M imidazole
Crystal Properties Matthews coefficient Solvent content 2.18 43.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.209 α = 90 b = 101.14 β = 105.626 c = 77.877 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2017-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 48.79 98.9 0.0486 16.47 6.85 105114
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.295
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2J80 1.7 48.79 104973 5202 99.866 0.168 0.1666 0.1958 0.2118 24.204
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] 0.333 -0.513 0.145 -0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.375 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_3_deg 13.369 r_lrange_it 6.373 r_lrange_other 6.373 r_dihedral_angle_1_deg 6.252 r_scangle_it 5.174 r_scangle_other 5.173 r_scbond_other 3.454 r_scbond_it 3.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.375 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_3_deg 13.369 r_lrange_it 6.373 r_lrange_other 6.373 r_dihedral_angle_1_deg 6.252 r_scangle_it 5.174 r_scangle_other 5.173 r_scbond_other 3.454 r_scbond_it 3.453 r_mcangle_it 2.891 r_mcangle_other 2.89 r_angle_other_deg 2.343 r_mcbond_other 2.151 r_mcbond_it 2.15 r_angle_refined_deg 1.65 r_nbd_other 0.248 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_refined 0.216 r_symmetry_nbd_other 0.215 r_symmetry_nbd_refined 0.2 r_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.129 r_ncsr_local_group_3 0.113 r_ncsr_local_group_8 0.111 r_ncsr_local_group_2 0.109 r_ncsr_local_group_21 0.105 r_ncsr_local_group_9 0.104 r_ncsr_local_group_5 0.102 r_ncsr_local_group_15 0.1 r_ncsr_local_group_11 0.098 r_ncsr_local_group_13 0.098 r_ncsr_local_group_7 0.097 r_ncsr_local_group_19 0.097 r_ncsr_local_group_17 0.096 r_ncsr_local_group_26 0.095 r_ncsr_local_group_28 0.095 r_ncsr_local_group_1 0.092 r_ncsr_local_group_23 0.086 r_chiral_restr 0.085 r_ncsr_local_group_4 0.084 r_ncsr_local_group_25 0.084 r_ncsr_local_group_12 0.082 r_ncsr_local_group_20 0.08 r_ncsr_local_group_6 0.078 r_ncsr_local_group_14 0.075 r_ncsr_local_group_10 0.071 r_ncsr_local_group_16 0.069 r_ncsr_local_group_22 0.069 r_ncsr_local_group_24 0.069 r_symmetry_nbtor_other 0.067 r_ncsr_local_group_18 0.066 r_ncsr_local_group_27 0.051 r_bond_other_d 0.035 r_gen_planes_other 0.021 r_xyhbond_nbd_other 0.013 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7635 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing