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Crystal Structure of DtxR(E9A C102D) Complexed with Nickel(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.755 α = 90 b = 61.755 β = 90 c = 104.557 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 2006-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-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 2.1 35 98.44 0.087 12 17.9 13090 33
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) 2.1 2.18 96.67 0.6 6.24 16.9 933
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 1P92 2.1 34.86 13090 686 98.44 0.19667 0.19361 0.1983 0.25599 0.2581 RANDOM 32.932
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 39.416 r_dihedral_angle_4_deg 21.423 r_dihedral_angle_3_deg 17.369 r_dihedral_angle_1_deg 7.375 r_scangle_it 6.279 r_scbond_it 4.061 r_mcangle_it 2.37 r_angle_refined_deg 2.221 r_mcbond_it 1.556 r_symmetry_hbond_refined 0.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.416 r_dihedral_angle_4_deg 21.423 r_dihedral_angle_3_deg 17.369 r_dihedral_angle_1_deg 7.375 r_scangle_it 6.279 r_scbond_it 4.061 r_mcangle_it 2.37 r_angle_refined_deg 2.221 r_mcbond_it 1.556 r_symmetry_hbond_refined 0.357 r_nbtor_refined 0.308 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.259 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.172 r_bond_refined_d 0.028 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1705 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing