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Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQ9 PDB entry 2QQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.95 M Sodium/Potasium Phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.8 α = 90 b = 63.8 β = 90 c = 108.165 γ = 120
Symmetry Space Group P 31 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 MARMOSAIC 300 mm CCD 2008-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.03313 APS 21-ID-D
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 1.85 50 99.2 0.079 26.628 10.4 21162 22293 34.1
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) 1.85 1.97 92.2 0.492 3.5 7 1880
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 2QQ9 1.85 38.65 22265 1135 99.58 0.224 0.221 0.2228 0.271 0.2697 RANDOM 34.099
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.878 r_dihedral_angle_3_deg 17.83 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_1_deg 5.792 r_scangle_it 4.827 r_scbond_it 3.035 r_mcangle_it 1.912 r_angle_refined_deg 1.667 r_mcbond_it 1.102 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.878 r_dihedral_angle_3_deg 17.83 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_1_deg 5.792 r_scangle_it 4.827 r_scbond_it 3.035 r_mcangle_it 1.912 r_angle_refined_deg 1.667 r_mcbond_it 1.102 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1688 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection