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Structural basis for specific inhibition of extracellular activation of pro/latent myostatin by SRK-015
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GGU PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU experimental model PDB 5F3H PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU experimental model PDB 3HH2 PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU experimental model PDB 3RJR PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU experimental model PDB 5NTU PDB entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 296 0.1 M sodium citrate, pH 5.5, 20% PEG3350, 15% 2-propanol, 3% trimethylamine N-oxide
Crystal Properties Matthews coefficient Solvent content 2.7 54.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.62 α = 90 b = 110.01 β = 90 c = 293.27 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 6M 2017-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.79 146.63 100 0.079 0.035 14.1 5.1 49196 79.718
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.84 100 1.487 0.645 1.2 5.3
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 entries 5GGU, 5F3H, 3HH2, 3RJR, & 5NTU 2.79 40.43 46728 2372 99.81 0.2193 0.217 0.2204 0.2643 0.2617 RANDOM 98.061
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] -2.55 3.06 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.928 r_dihedral_angle_4_deg 18.807 r_dihedral_angle_3_deg 18.752 r_dihedral_angle_1_deg 9.111 r_angle_refined_deg 2.072 r_angle_other_deg 1.171 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.928 r_dihedral_angle_4_deg 18.807 r_dihedral_angle_3_deg 18.752 r_dihedral_angle_1_deg 9.111 r_angle_refined_deg 2.072 r_angle_other_deg 1.171 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10841 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction