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N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NC7 PDB ENTRY 4NC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290.15 2M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K 2 VAPOR DIFFUSION, HANGING DROP 8.2 290.15 1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.462 α = 90 b = 109.636 β = 90 c = 82.928 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX-225 2012-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9871 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.16 41.5 98.9 9941 9786 2 2
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 2.17 2.28 95.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4NC7 2.17 41.5 2 9762 9317 470 98.43 0.267 0.22682 0.22391 0.2289 0.28263 0.2807 RANDOM 56.528
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] 4.99 -2.62 -2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.788 r_dihedral_angle_4_deg 19.34 r_dihedral_angle_3_deg 15.945 r_dihedral_angle_1_deg 6.474 r_angle_refined_deg 1.54 r_angle_other_deg 0.784 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.788 r_dihedral_angle_4_deg 19.34 r_dihedral_angle_3_deg 15.945 r_dihedral_angle_1_deg 6.474 r_angle_refined_deg 1.54 r_angle_other_deg 0.784 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1314 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 2
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling