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Crystal Structure of a Thermophilic Serpin, Tengpin, in the Latent State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SNG PDB ENTRY 1SNG, THERMOPIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 294 28% PEG 400, 0.1 M Na Hepes, 0.2 M Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.89 35.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.762 α = 90 b = 44.907 β = 90 c = 159.233 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 4 2004-09-24 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 Merge 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 1.6 79 98.4 0.076 20.1 5.4 42797 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 1.6 1.66 98.1 0.351 1.6 1.6
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 PDB ENTRY 1SNG, THERMOPIN 1.6 79 40547 2138 98.5 0.208 0.206 0.2076 0.253 0.2515 RANDOM 17.58
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] -0.08 0.23 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.556 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_3_deg 11.854 r_dihedral_angle_1_deg 5.091 r_scangle_it 3.036 r_scbond_it 2.202 r_mcangle_it 1.281 r_angle_refined_deg 0.999 r_mcbond_it 0.799 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.556 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_3_deg 11.854 r_dihedral_angle_1_deg 5.091 r_scangle_it 3.036 r_scbond_it 2.202 r_mcangle_it 1.281 r_angle_refined_deg 0.999 r_mcbond_it 0.799 r_nbtor_refined 0.3 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.089 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_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 2841 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling