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Structure of the copper sensitive operon repressor from Streptomyces lividans at pH6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ADZ PDB ENTRY 4ADZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.01 M MAGNESIUM SULFATE, 0.05 M SODIUM CACODYLATE PH 6.0, 1.8 M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.74 α = 90 b = 89.74 β = 90 c = 103.86 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M MIRRORS 2013-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 40.2 99.7 0.05 15.7 4.9 14603
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 2.05 99.8 0.73 2.3 4.5
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 4ADZ 2 67.9 13875 716 99.48 0.21198 0.21086 0.2179 0.23364 0.2473 RANDOM 39.342
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] -0.86 -0.86 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_3_deg 15.566 r_dihedral_angle_4_deg 6.952 r_dihedral_angle_1_deg 4.84 r_scbond_it 4.308 r_mcangle_it 4.174 r_mcbond_it 3.19 r_mcbond_other 3.155 r_angle_refined_deg 1.499 r_angle_other_deg 0.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_3_deg 15.566 r_dihedral_angle_4_deg 6.952 r_dihedral_angle_1_deg 4.84 r_scbond_it 4.308 r_mcangle_it 4.174 r_mcbond_it 3.19 r_mcbond_other 3.155 r_angle_refined_deg 1.499 r_angle_other_deg 0.965 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other 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 721 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing