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Structure of a PhoP-DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R0J PDB entries 3R0J & 1GXP experimental model PDB 1GXP PDB entries 3R0J & 1GXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 50 mM sodium cacodylate, pH 6.5, 10 mM calcium chloride, 12% PEG4000, 2 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.24 α = 90 b = 98.176 β = 90 c = 167.888 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2013-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.4 30 90 0.112 0.117 0.033 9.7 11.6 55326 67.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 54.2 0.712 0.768 0.279 0.932 2.13 6.1 1642
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 entries 3R0J & 1GXP 2.4 29.6 55261 2793 89.38 0.1849 0.1827 0.1837 0.2265 0.2275 RANDOM 86.86
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] -28.4723 -0.7463 29.2186
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.53 t_omega_torsion 3.2 t_angle_deg 1.11 t_bond_d 0.011 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.53 t_omega_torsion 3.2 t_angle_deg 1.11 t_bond_d 0.011 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6937 Nucleic Acid Atoms 2120 Solvent Atoms 233 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction PHASER phasing Coot model building HKL-2000 data reduction