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Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and thymine (T)
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 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.9 α = 90 b = 156.318 β = 91.77 c = 76.028 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 2014-05-18 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) 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 2.05 50 99.9 0.085 10.1 3.8 82717 28.5
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 2.05 2.12 100 0.468 3 3.8 8246
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5C3O 2.05 50 78516 4130 99.76 0.1856 0.1841 0.2148 0.2218 RANDOM 35.67
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] 0.91 0.39 -0.19 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.964 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_4_deg 12.321 r_dihedral_angle_1_deg 5.568 r_angle_other_deg 3.567 r_angle_refined_deg 0.977 r_chiral_restr 0.056 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 34.964 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_4_deg 12.321 r_dihedral_angle_1_deg 5.568 r_angle_other_deg 3.567 r_angle_refined_deg 0.977 r_chiral_restr 0.056 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 10183 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 144
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction