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The 2.1 A structure of a tumour suppressing serpin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 295 0.1M BisTris, 2.9M (NH4)2SO4, 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 = 54.115 α = 90 b = 95.047 β = 90 c = 139.225 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 OSMIC MIRRORS 2004-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 78.6 99.8 0.045 0.045 22.2 36.8 42714 42714 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XU8 2.1 78.57 139.225 40352 40352 2136 99.62 0.20729 0.20729 0.20502 0.2222 0.24933 0.2595 RANDOM 40.632
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] 0.42 -0.23 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.427 r_dihedral_angle_4_deg 18.406 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_1_deg 5.52 r_scangle_it 4.843 r_scbond_it 3.34 r_mcangle_it 2.039 r_mcbond_it 1.191 r_angle_refined_deg 1.152 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.427 r_dihedral_angle_4_deg 18.406 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_1_deg 5.52 r_scangle_it 4.843 r_scbond_it 3.34 r_mcangle_it 2.039 r_mcbond_it 1.191 r_angle_refined_deg 1.152 r_nbtor_refined 0.3 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.076 r_bond_refined_d 0.008 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 5523 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing