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DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPR APO-DTXR (PDB ENTRY 1DPR)
Crystallization Crystal Properties Matthews coefficient Solvent content 4.03 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.5 α = 90 b = 64.5 β = 90 c = 105.7 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 277 IMAGE PLATE RIGAKU 1995-06-01 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 2.32 55 80.6 0.041 2.8 9464 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER THROUGHOUT APO-DTXR (PDB ENTRY 1DPR) 2.4 8 2 8425 897 84 0.246 0.246 0.321 RANDOM 27
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.4 x_angle_deg 1.33 x_improper_angle_d 0.69 x_bond_d 0.012 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.4 x_angle_deg 1.33 x_improper_angle_d 0.69 x_bond_d 0.012 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1101 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 2
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement R-AXIS data reduction R-AXIS data scaling X-PLOR phasing