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Crystal Structure of Salivary Cystatin from the Soft Tick Ornithodoros moubata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LH4 PDB ENTRY 3LH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES pH 7.5, 1.5M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.6 65.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.805 α = 90 b = 69.805 β = 90 c = 133.994 γ = 120
Symmetry Space Group P 31 2 1
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 0.954 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 50 98.8 0.057 27.3 5.6 14369 53.4
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) 2.45 2.54 90 0.334 2.4 3.8 1285
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 3LH4 2.45 30.95 13588 744 98.86 0.18937 0.1875 0.1904 0.22312 0.228 RANDOM 39.921
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] -1.03 -0.52 -1.03 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.682 r_dihedral_angle_4_deg 23.203 r_dihedral_angle_3_deg 16.687 r_dihedral_angle_1_deg 7.102 r_scangle_it 2.053 r_scbond_it 1.316 r_angle_refined_deg 1.256 r_mcangle_it 0.796 r_mcbond_it 0.471 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.682 r_dihedral_angle_4_deg 23.203 r_dihedral_angle_3_deg 16.687 r_dihedral_angle_1_deg 7.102 r_scangle_it 2.053 r_scbond_it 1.316 r_angle_refined_deg 1.256 r_mcangle_it 0.796 r_mcbond_it 0.471 r_nbtor_refined 0.304 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.145 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.076 r_symmetry_hbond_refined 0.042 r_bond_refined_d 0.012 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 1698 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 20
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling