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Crystal structure of Tpn2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.01 M Zin sulfate heptahydrate, 0.1 M MES monohydrate, ph 6.5, 25% polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.539 α = 90 b = 92.539 β = 90 c = 127.911 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX300HE 2019-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.9732 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.57 30 99.3 0.12 0.84 15.66 4.7 38716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.67 100 0.603 0.711 3.8 5.6
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 5BP8 2.57 27.39 36668 2048 99.25 0.2548 0.2529 0.2561 0.2879 0.2884 RANDOM 53.781
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 -0.02 -0.04 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_3_deg 21.523 r_dihedral_angle_4_deg 19.781 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.324 r_angle_other_deg 1.278 r_chiral_restr 0.061 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_3_deg 21.523 r_dihedral_angle_4_deg 19.781 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.324 r_angle_other_deg 1.278 r_chiral_restr 0.061 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7443 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing HKL-2000 data reduction