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Crystal Structure Of The Calcium-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator KdpE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XHF PDB ENTRY 1XHF (Ala Model)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 8000, Calcium Acetate, MES Buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.372 α = 90 b = 127.162 β = 90 c = 65.207 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 4 2004-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 1.07179 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 30 100 0.063 48 13.6 20179 20163 -3 12.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 99.9 0.159 24.2 10.2 1992
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1XHF (Ala Model) 2 30 20162 18100 2046 99.99 0.19831 0.19334 0.1956 0.24184 0.2447 RANDOM 25.051
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] -1.03 1.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.585 r_scangle_it 3.099 r_mcangle_it 2.599 r_scbond_it 1.929 r_angle_refined_deg 1.556 r_mcbond_it 1.536 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.585 r_scangle_it 3.099 r_mcangle_it 2.599 r_scbond_it 1.929 r_angle_refined_deg 1.556 r_mcbond_it 1.536 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.2 r_chiral_restr 0.118 r_metal_ion_refined 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1869 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing