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Crystal structure of Pun g 1.0101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 298 0.1 M sodium acetate, pH 4.6 and 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.522 α = 90 b = 89.424 β = 102.79 c = 58.94 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 MX300-HS 2017-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 90.6 0.22 0.124 6.6 2.8 10593
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 90.4 0.511 0.316 0.751 2.3 2
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 5TVI 2.4 35.32 10014 541 90.07 0.2064 0.2038 0.21 0.2519 0.2494 RANDOM 33.686
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] -1.84 0.11 -1.69 3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.555 r_dihedral_angle_4_deg 14.078 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 4.788 r_angle_other_deg 2.337 r_angle_refined_deg 1.483 r_chiral_restr 0.075 r_bond_other_d 0.036 r_bond_refined_d 0.01 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.555 r_dihedral_angle_4_deg 14.078 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 4.788 r_angle_other_deg 2.337 r_angle_refined_deg 1.483 r_chiral_restr 0.075 r_bond_other_d 0.036 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing