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Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 295 26 mg/mL protein, 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.74 α = 90 b = 57.74 β = 90 c = 184.27 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 CCD ADSC QUANTUM 315r 2018-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.47 55.1 100 0.069 0.072 0.02 0.999 21.6 12.9 27259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.49 100 0.501 0.529 0.17 0.928 9.6
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 2QCB 1.47 55.1 25837 1383 99.94 0.154 0.1528 0.152 0.1768 0.1768 RANDOM 17.436
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] 0.04 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.298 r_dihedral_angle_4_deg 15.426 r_dihedral_angle_3_deg 14.08 r_dihedral_angle_1_deg 6.976 r_angle_other_deg 3.725 r_angle_refined_deg 2.434 r_chiral_restr 0.134 r_bond_other_d 0.038 r_bond_refined_d 0.018 r_gen_planes_other 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.298 r_dihedral_angle_4_deg 15.426 r_dihedral_angle_3_deg 14.08 r_dihedral_angle_1_deg 6.976 r_angle_other_deg 3.725 r_angle_refined_deg 2.434 r_chiral_restr 0.134 r_bond_other_d 0.038 r_bond_refined_d 0.018 r_gen_planes_other 0.017 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 935 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 75
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing