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Crystallographic structure of the circularly permuted human Taspase1 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 0.1 M sodium citrate pH 4.0, 1.0 M ammonium sulfate, 10% 2-methyl-2,4-pentanediol (MPD), and 0.4 M NaCl
Crystal Properties Matthews coefficient Solvent content 4.3 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196 α = 90 b = 196 β = 90 c = 196.91 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 100 PIXEL DECTRIS PILATUS3 S 6M 2017-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 3.04 49.05 93.9 0.068 1 21.2 19.6 15315
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 3.04 3.11 1.8
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 6UGK 3.04 49.05 13749 1568 54.35 0.2435 0.2366 0.2663 0.3074 0.3268 RANDOM 152.987
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_3_deg 22.097 r_dihedral_angle_4_deg 17.522 r_dihedral_angle_1_deg 8.392 r_angle_other_deg 2.469 r_angle_refined_deg 1.744 r_chiral_restr 0.066 r_bond_other_d 0.036 r_bond_refined_d 0.007 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_3_deg 22.097 r_dihedral_angle_4_deg 17.522 r_dihedral_angle_1_deg 8.392 r_angle_other_deg 2.469 r_angle_refined_deg 1.744 r_chiral_restr 0.066 r_bond_other_d 0.036 r_bond_refined_d 0.007 r_gen_planes_other 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5349 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing