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Crystal Structure of DtxR(M10A 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 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.32 α = 90 b = 62.32 β = 90 c = 104.582 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 OXFORD ONYX CCD 2006-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA
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 1.92 29.87 90 0.114 6.01 7.2 15860 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.92 1.97 41.69 537
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1P92 1.92 29.87 15860 853 90.12 0.22871 0.22437 0.31103 0.2746 RANDOM 23.427
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.369 r_dihedral_angle_4_deg 20.194 r_dihedral_angle_3_deg 19.735 r_dihedral_angle_1_deg 7.834 r_scangle_it 4.264 r_scbond_it 3.225 r_angle_refined_deg 2.53 r_mcangle_it 1.885 r_mcbond_it 1.301 r_symmetry_hbond_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.369 r_dihedral_angle_4_deg 20.194 r_dihedral_angle_3_deg 19.735 r_dihedral_angle_1_deg 7.834 r_scangle_it 4.264 r_scbond_it 3.225 r_angle_refined_deg 2.53 r_mcangle_it 1.885 r_mcbond_it 1.301 r_symmetry_hbond_refined 0.34 r_nbtor_refined 0.302 r_nbd_refined 0.269 r_symmetry_vdw_refined 0.237 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.212 r_bond_refined_d 0.028 r_gen_planes_refined 0.01 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 1708 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection MOSFLM data reduction SCALA data scaling PHASER phasing