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Crystal structure of Geodia cydonium sponge adhesion molecule long form (SAML).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 PEG4000, 0.2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.08 α = 90 b = 41.16 β = 90.009 c = 77.801 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2022-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.61 77.8 99.5 0.067 0.088 0.056 0.997 9.3 4.1 27255 20.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.64 99.6 0.74 0.576 1.5 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.61 38.931 27237 1317 99.431 0.153 0.1509 0.1638 0.2027 0.2108 27.475
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] -0.307 0.021 -1.084 1.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.996 r_dihedral_angle_3_deg 11.247 r_dihedral_angle_1_deg 7.359 r_dihedral_angle_2_deg 4.539 r_lrange_it 4.387 r_lrange_other 4.386 r_rigid_bond_restr 4.066 r_mcangle_it 3.199 r_mcangle_other 3.199 r_scangle_it 2.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.996 r_dihedral_angle_3_deg 11.247 r_dihedral_angle_1_deg 7.359 r_dihedral_angle_2_deg 4.539 r_lrange_it 4.387 r_lrange_other 4.386 r_rigid_bond_restr 4.066 r_mcangle_it 3.199 r_mcangle_other 3.199 r_scangle_it 2.763 r_scangle_other 2.75 r_mcbond_it 2.293 r_mcbond_other 2.289 r_scbond_it 2.052 r_scbond_other 2.046 r_angle_refined_deg 1.554 r_angle_other_deg 0.554 r_xyhbond_nbd_refined 0.227 r_nbd_other 0.225 r_nbd_refined 0.217 r_symmetry_nbd_other 0.214 r_symmetry_nbd_refined 0.207 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.123 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1493 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing