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Crystal structure of perlecan region 3 mutant (P1019L) construct I876-V1272 including one laminin IV-like and four laminin EGF-like domains.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295.15 0.85M succinic acid, pH 7
Crystal Properties Matthews coefficient Solvent content 3.79 67.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.65 α = 75.235 b = 74.968 β = 73.124 c = 81.368 γ = 80.112
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 2024-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7293 MAX IV BioMAX
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 2.52 47.67 98.5 0.994 9.9 3.6 41874
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 2.52 2.58 0.645
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 2.52 47.67 41722 1993 98.545 0.19 0.1883 0.1883 0.2202 0.2203 58.623
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] -3.371 1.5 0.306 -1.314 -2.903 3.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.386 r_dihedral_angle_6_deg 14.258 r_lrange_it 10.07 r_dihedral_angle_1_deg 7.82 r_scangle_it 7.035 r_dihedral_angle_2_deg 6.725 r_mcangle_it 4.888 r_scbond_it 4.578 r_mcbond_it 3.073 r_angle_refined_deg 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.386 r_dihedral_angle_6_deg 14.258 r_lrange_it 10.07 r_dihedral_angle_1_deg 7.82 r_scangle_it 7.035 r_dihedral_angle_2_deg 6.725 r_mcangle_it 4.888 r_scbond_it 4.578 r_mcbond_it 3.073 r_angle_refined_deg 1.87 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.163 r_chiral_restr 0.127 r_ncsr_local_group_1 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5063 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing