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Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and 5-hydroxymethyluracil (5hmU)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.1 M BIS-TRIS, 25%(W/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.817 α = 90 b = 155.775 β = 91.65 c = 75.992 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE 2014-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.35 50 98.3 0.069 0.083 0.046 15.3 3.1 53781 25.2
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 2.35 2.43 99.4 0.126 0.152 0.084 0.973 10.2 3.1 5427
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 5C3O 2.35 50 51062 2689 98.17 0.1826 0.1805 0.1846 0.2245 0.2257 RANDOM 30.573
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] 0.36 0.26 -0.37 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_3_deg 13.326 r_dihedral_angle_4_deg 13.031 r_dihedral_angle_1_deg 5.56 r_angle_other_deg 3.57 r_angle_refined_deg 0.989 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_3_deg 13.326 r_dihedral_angle_4_deg 13.031 r_dihedral_angle_1_deg 5.56 r_angle_other_deg 3.57 r_angle_refined_deg 0.989 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10140 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 136
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction