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Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R1J PDB entry 2R1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 PEG 400, Thallium acetate, Tris-HCl, Magnesium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.82 67.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.249 α = 90 b = 64.249 β = 90 c = 100.82 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 225 mm CCD 2008-03-05 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97784 APS 22-BM
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 1.9 30.61 98.5 0.073 44.3 13.4 31737 31737
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) 1.9 1.95 97.7 0.487 9.29 11.3 1591
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2R1J 1.9 30.61 1 30146 1591 98.54 0.185 0.184 0.1803 0.208 0.2072 RANDOM 25.067
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.494 r_dihedral_angle_3_deg 12.307 r_dihedral_angle_4_deg 8.036 r_dihedral_angle_1_deg 4.085 r_scangle_it 3.22 r_scbond_it 2.122 r_angle_refined_deg 1.681 r_mcangle_it 1.468 r_mcbond_it 0.932 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.494 r_dihedral_angle_3_deg 12.307 r_dihedral_angle_4_deg 8.036 r_dihedral_angle_1_deg 4.085 r_scangle_it 3.22 r_scbond_it 2.122 r_angle_refined_deg 1.681 r_mcangle_it 1.468 r_mcbond_it 0.932 r_nbtor_refined 0.294 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.11 r_symmetry_vdw_refined 0.106 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1030 Nucleic Acid Atoms 814 Solvent Atoms 279 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing