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Crystal Structure of Silicatein Alpha from Marine Sponge Tethya aurantium
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VHS pdbid 2VHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 298 in vivo
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.6 α = 90 b = 59.6 β = 90 c = 116.29 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 PIXEL DECTRIS EIGER X 16M 2019-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.4 51.5 100 0.91 6.1 159 9827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.486 0.58
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 pdbid 2VHS 2.4 47.18 9337 492 99.87 0.2436 0.2403 0.2459 0.302 0.2994 RANDOM 49.104
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] 1.46 0.73 1.46 -4.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 17.532 r_dihedral_angle_3_deg 17.051 r_dihedral_angle_1_deg 6.237 r_angle_refined_deg 1.367 r_angle_other_deg 0.79 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 17.532 r_dihedral_angle_3_deg 17.051 r_dihedral_angle_1_deg 6.237 r_angle_refined_deg 1.367 r_angle_other_deg 0.79 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1586 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling MOLREP phasing