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Structure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in complex a palindromic DNA (P6422 space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 Terbutanol, Na-citrate, MgCl2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.18 α = 90 b = 179.18 β = 90 c = 96.74 γ = 120
Symmetry Space Group P 64 2 2
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 EIGER X 16M 2015-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.8 45.61 99.7 0.137 0.999 14.3 19.5 23104 101.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 0.388
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 6Z74 2.8 45.61 16349 817 70.8 0.189 0.188 0.2057 0.199 0.2209 RANDOM 83.94
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] 0.9199 0.9199 -1.8398
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.46 t_omega_torsion 2.22 t_angle_deg 1.01 t_bond_d 0.009 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 19.46 t_omega_torsion 2.22 t_angle_deg 1.01 t_bond_d 0.009 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 1821 Nucleic Acid Atoms 202 Solvent Atoms 23 Heterogen Atoms 25
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction