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Structure of Protease1 from Pyrococcus horikoshii in space group 19 with a hexamer in the asymmetric unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM tri-sodium citrate pH 5.6, 200 mM sodium potassium tartrate, 1.9 to 2.4 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.13 70.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.741 α = 90 b = 123.636 β = 90 c = 129.223 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2015-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.95 70.72 99.8 0.068 0.997 11.8 6.6 135285 25.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.05 0.673 0.567
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Q3T 1.95 18.59 1.34 134946 2000 99.76 0.1818 0.1815 0.1834 0.204 0.2052 30.88
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.7803 f_angle_d 1.1025 f_chiral_restr 0.0689 f_bond_d 0.0095 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7836 Nucleic Acid Atoms Solvent Atoms 1010 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement PHENIX refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing