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Crystal structure of secretory abundant heat soluble protein 4 from Ramazzottius varieornatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 50mM HEPES pH 7.8, 1mM ZnSO4, 24%(v/v) PEG600
Crystal Properties Matthews coefficient Solvent content 1.92 36.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.802 α = 89.97 b = 41.926 β = 80.75 c = 53.483 γ = 78.76
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 RAYONIX MX300HE 2017-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 50.01 95.9 0.036 0.051 0.036 23.1 2 42396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 95.5 0.26 0.368 0.26 0.818 2.9 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XNA 1.5 50.01 40319 2077 95.81 0.16161 0.15945 0.20308 0.2101 RANDOM 23.76
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.344 r_sphericity_free 28.975 r_dihedral_angle_4_deg 22.478 r_sphericity_bonded 17.686 r_dihedral_angle_3_deg 13.388 r_dihedral_angle_1_deg 5.634 r_long_range_B_refined 4.203 r_mcangle_it 2.25 r_scbond_it 1.692 r_mcbond_it 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.344 r_sphericity_free 28.975 r_dihedral_angle_4_deg 22.478 r_sphericity_bonded 17.686 r_dihedral_angle_3_deg 13.388 r_dihedral_angle_1_deg 5.634 r_long_range_B_refined 4.203 r_mcangle_it 2.25 r_scbond_it 1.692 r_mcbond_it 1.49 r_angle_refined_deg 1.224 r_rigid_bond_restr 0.91 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2324 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing