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Crystal Structure of a Thermophilic Serpin, Tengpin, in the Native State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PEF PDB ENTRIES 2PEF, 1SNG experimental model PDB 1SNG PDB ENTRIES 2PEF, 1SNG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 294 2M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.93 75.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.939 α = 90 b = 217.939 β = 90 c = 217.939 γ = 90
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 4 2005-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.7 154 97.8 7.7 14.4 3 43616 3
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 2.7 2.8 98.1 0.66 2.2 2.7
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 PDB ENTRIES 2PEF, 1SNG 2.7 154 43616 2321 97.8 0.197 0.195 0.1926 0.235 0.2263 RANDOM 58.44
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 r_dihedral_angle_2_deg 36.815 r_dihedral_angle_4_deg 25.209 r_angle_other_deg 18.181 r_dihedral_angle_3_deg 17.804 r_dihedral_angle_1_deg 6.389 r_scangle_it 5.741 r_scbond_it 3.796 r_mcangle_it 2.314 r_angle_refined_deg 1.502 r_mcbond_it 1.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.815 r_dihedral_angle_4_deg 25.209 r_angle_other_deg 18.181 r_dihedral_angle_3_deg 17.804 r_dihedral_angle_1_deg 6.389 r_scangle_it 5.741 r_scbond_it 3.796 r_mcangle_it 2.314 r_angle_refined_deg 1.502 r_mcbond_it 1.372 r_nbtor_refined 0.311 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.098 r_nbd_other 0.068 r_nbtor_other 0.025 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5895 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing