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Crystal Structure Of The Mg+2/BeF3-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 1ZH3 PDB ENTRY 1ZH3 (Ala Model)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 8000, Magnesium Chloride, MES Buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.912 α = 90 b = 126.675 β = 90 c = 62.655 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 2004-11-12 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 2.2 30 96.8 0.048 30.1 5.4 15063 14572 -3 26.4
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 2.28 88.9 0.213 7.8 4.9 1316
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 1ZH3 (Ala Model) 2.2 30 15170 13343 706 95.68 0.22851 0.22651 0.2258 0.26507 0.2656 RANDOM 45.01
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] -2.73 -1.35 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.82 r_mcangle_it 2.53 r_scangle_it 2.515 r_angle_refined_deg 1.653 r_scbond_it 1.602 r_mcbond_it 1.501 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.257 r_symmetry_hbond_refined 0.231 r_xyhbond_nbd_refined 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.82 r_mcangle_it 2.53 r_scangle_it 2.515 r_angle_refined_deg 1.653 r_scbond_it 1.602 r_mcbond_it 1.501 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.257 r_symmetry_hbond_refined 0.231 r_xyhbond_nbd_refined 0.223 r_chiral_restr 0.11 r_metal_ion_refined 0.046 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1866 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing