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Crystal structure of serpin from tick Ixodes ricinus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20mM HEPES pH 7.2, 0.075M MES pH 6.5, 9 % (w/v) PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.575 α = 90 b = 84.575 β = 90 c = 124.412 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 MARMOSAIC 225 mm CCD 2009-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.953 EMBL/DESY, HAMBURG X12
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 1.8 84.52 99.6 0.046 32.8 3.8 80571 80249 23.2
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 1.8 1.86 97.3 0.358 2.3 3.3 7790
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 1HLE 1.8 30 76177 4026 99.62 0.17283 0.17073 0.2178 0.21222 0.2499 RANDOM 26.216
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] -0.87 -0.87 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.643 r_dihedral_angle_3_deg 13.15 r_dihedral_angle_4_deg 12.724 r_dihedral_angle_1_deg 6.028 r_scangle_it 2.538 r_scbond_it 1.59 r_angle_refined_deg 1.22 r_mcangle_it 0.883 r_mcbond_it 0.562 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.643 r_dihedral_angle_3_deg 13.15 r_dihedral_angle_4_deg 12.724 r_dihedral_angle_1_deg 6.028 r_scangle_it 2.538 r_scbond_it 1.59 r_angle_refined_deg 1.22 r_mcangle_it 0.883 r_mcbond_it 0.562 r_nbtor_refined 0.304 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 5898 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms 16
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling