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Structure of Pfp1 protease from Thermococcus thioreducens: large cell H3 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.4 M Sodium Citrate, pH 6.5, vapor diffusion, sitting drop
Crystal Properties Matthews coefficient Solvent content 2.528 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.85 α = 90 b = 152.85 β = 90 c = 82.541 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 298 CCD RIGAKU SATURN 944+ Osmic mirrors 2013-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 1.86 38.22 86.3 0.123 0.992 11.9 8.8 52126 15.88
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 1.86 1.9 33.5 0.583 0.485 0.6 1
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 1G2I 1.86 38.22 49624 2499 86.27 0.12962 0.1274 0.128 0.1734 0.1742 RANDOM 20.02
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] -0.11 -0.06 -0.11 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.176 r_dihedral_angle_4_deg 21.643 r_dihedral_angle_3_deg 15.169 r_long_range_B_refined 11.307 r_long_range_B_other 11.17 r_scangle_other 8.535 r_dihedral_angle_1_deg 7.896 r_scbond_it 5.693 r_scbond_other 5.691 r_mcangle_it 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.176 r_dihedral_angle_4_deg 21.643 r_dihedral_angle_3_deg 15.169 r_long_range_B_refined 11.307 r_long_range_B_other 11.17 r_scangle_other 8.535 r_dihedral_angle_1_deg 7.896 r_scbond_it 5.693 r_scbond_other 5.691 r_mcangle_it 3.675 r_mcangle_other 3.675 r_mcbond_it 2.718 r_mcbond_other 2.707 r_angle_refined_deg 1.23 r_angle_other_deg 0.628 r_chiral_restr 0.078 r_gen_planes_refined 0.02 r_bond_refined_d 0.009 r_gen_planes_other 0.002 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5196 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling CNS phasing REFMAC refinement Coot model building