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DNA-bound form of TetR-like repressor SimR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y2Z PDB ENTRY 2Y2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 200 MICROMOLAR AND DNA AT 200 MICROMOLAR WERE MIXED WITH 10% PEG 8000, 0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE IN 0.05 M SODIUM CACODYLATE PH6.5 IN A 1:1 RATIO
Crystal Properties Matthews coefficient Solvent content 2.79 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.788 α = 90 b = 112.613 β = 90 c = 163.725 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 CCD ADSC QUANTUM 315r 2010-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.99 92.78 95.2 0.01 8.3 3.1 31030 -3 53.4
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 2.99 3.15 96.5 0.59 1.8 3.1
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 2Y2Z 2.99 92.78 29372 1576 94.31 0.21159 0.20954 0.2118 0.25103 0.2515 RANDOM 57.4
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] 3.69 -6.67 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.973 r_dihedral_angle_3_deg 17.183 r_dihedral_angle_4_deg 13.94 r_dihedral_angle_1_deg 4.593 r_angle_refined_deg 1.222 r_angle_other_deg 1.093 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.973 r_dihedral_angle_3_deg 17.183 r_dihedral_angle_4_deg 13.94 r_dihedral_angle_1_deg 4.593 r_angle_refined_deg 1.222 r_angle_other_deg 1.093 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7161 Nucleic Acid Atoms 1382 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing