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Structure of a Thermophilic Serpin in the Native State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MTP Regions of the PDB entry 1MTP predicted to remain relatively unchanged in the native state (residues 5-78; 168-309; 333-367).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 30% PEG 4K, 0.2 M Ammonium Sulfate, 0.1 M Sodium Cacodylate. Additive 0.1 M L-cysteine to drop. , pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.354 α = 90 b = 81.171 β = 90 c = 106.625 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 298 CCD ADSC QUANTUM 4 mirrors 2003-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 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 1.76 26.2 0.084 14.6 3.4 37435 37423 2 2
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) 1.76 1.8 98.6 0.425 2.8 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Regions of the PDB entry 1MTP predicted to remain relatively unchanged in the native state (residues 5-78; 168-309; 333-367). 1.76 26.2 37435 37423 1981 98.27 0.18775 0.18591 0.1996 0.22255 0.2348 RANDOM 14.865
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] -0.31 -0.05 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.086 r_dihedral_angle_4_deg 13.639 r_dihedral_angle_3_deg 12.192 r_dihedral_angle_1_deg 5.212 r_scangle_it 3.586 r_scbond_it 2.411 r_mcangle_it 1.598 r_angle_refined_deg 1.032 r_mcbond_it 1.019 r_angle_other_deg 0.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.086 r_dihedral_angle_4_deg 13.639 r_dihedral_angle_3_deg 12.192 r_dihedral_angle_1_deg 5.212 r_scangle_it 3.586 r_scbond_it 2.411 r_mcangle_it 1.598 r_angle_refined_deg 1.032 r_mcbond_it 1.019 r_angle_other_deg 0.717 r_mcbond_other 0.191 r_nbd_refined 0.187 r_symmetry_vdw_other 0.179 r_nbd_other 0.173 r_nbtor_refined 0.167 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.108 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.078 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2742 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing