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The 2.8 A structure of a tumour suppressing serpin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OVA PDB ENTRY 1OVA CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 295 Ammonium sulfate, Bis-Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.54 α = 90 b = 100.48 β = 90 c = 136.61 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 IMAGE PLATE RIGAKU RAXIS IV Mirrors 2004-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.8 50 96.9 0.088 11.5 2.8 18753 18174 1
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) 2.8 2.9 93.7 0.322 3.2 2.4 1711
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 PDB ENTRY 1OVA CHAIN A 2.8 20 18753 17231 945 96.91 0.22409 0.2207 0.2388 0.28568 0.2981 RANDOM 43.129
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] 0.65 1.2 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.784 r_dihedral_angle_4_deg 22.227 r_dihedral_angle_3_deg 18.733 r_dihedral_angle_1_deg 6.163 r_scangle_it 5.045 r_scbond_it 3.188 r_mcangle_it 1.889 r_angle_refined_deg 1.28 r_mcbond_it 1.071 r_symmetry_hbond_refined 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.784 r_dihedral_angle_4_deg 22.227 r_dihedral_angle_3_deg 18.733 r_dihedral_angle_1_deg 6.163 r_scangle_it 5.045 r_scbond_it 3.188 r_mcangle_it 1.889 r_angle_refined_deg 1.28 r_mcbond_it 1.071 r_symmetry_hbond_refined 0.38 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.265 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5815 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing CNS refinement REFMAC refinement