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Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and 5-formyluracil (5fU)
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 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.801 α = 90 b = 155.604 β = 91.74 c = 75.954 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 2014-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9199 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 2.15 50 98.5 0.123 0.14 0.068 8.4 4.2 69438 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 2.15 2.23 97.1 0.594 0.68 0.33 0.758 3.7 4.1 6848
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 2.15 50 66062 3343 98.14 0.1861 0.1839 0.1862 0.2278 0.2311 RANDOM 34.027
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] 0.26 0.62 -0.96 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.9 r_dihedral_angle_4_deg 15.881 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 5.659 r_mcangle_it 2.143 r_mcbond_it 1.21 r_mcbond_other 1.21 r_angle_refined_deg 1.058 r_angle_other_deg 0.748 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.9 r_dihedral_angle_4_deg 15.881 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 5.659 r_mcangle_it 2.143 r_mcbond_it 1.21 r_mcbond_other 1.21 r_angle_refined_deg 1.058 r_angle_other_deg 0.748 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10145 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction