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Crystal structure of the DNA-binding domain of PhoP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGS PDB entry 1KGS C-terminal domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 1.4 M Na/K phosphate, pH 5.6, 100 mM glycine, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.884 α = 90 b = 101.129 β = 126.72 c = 86.93 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 210 2006-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9795 NSLS X6A
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 1.779 20 94.8 0.036 18.6 2.9 65220
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 1.779 1.84 96.7 0.582 2.03 2.7 6629
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 PDB entry 1KGS C-terminal domain 1.779 20 65210 3310 94.63 0.198 0.196 0.2529 0.238 0.2828 RANDOM 41.509
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] 0.35 0.43 -0.48 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.006 r_dihedral_angle_4_deg 19.734 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_1_deg 5.719 r_scangle_it 4.449 r_mcangle_it 3.729 r_scbond_it 3.185 r_mcbond_it 2.594 r_angle_refined_deg 1.554 r_metal_ion_refined 0.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.006 r_dihedral_angle_4_deg 19.734 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_1_deg 5.719 r_scangle_it 4.449 r_mcangle_it 3.729 r_scbond_it 3.185 r_mcbond_it 2.594 r_angle_refined_deg 1.554 r_metal_ion_refined 0.378 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.117 r_symmetry_metal_ion_refined 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4796 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing