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Crystal structure of the G2 domain of Agrin from Mus Musculus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other solved using SAD model from ARP/wARP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294 100mM sodium acetate, 15% PEG 20000, pH 4.6, Vapor diffusion, sitting drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.98 38.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.62 α = 72.28 b = 45.58 β = 68.53 c = 51.51 γ = 65.44
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 MX225HE 2010-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.4 47.16 93.3 0.093 7.6 3.9 57584 13.136
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.48 92.6 0.491 2.3 3.9 8386
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 SAD THROUGHOUT ARP/wARP 1.4 36.38 57556 2946 100 0.194 0.1921 0.1951 0.2289 0.2309 RANDOM 17.1416
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] 0.03 -0.01 -0.02 0.04 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.521 r_dihedral_angle_4_deg 19.498 r_dihedral_angle_1_deg 13.458 r_dihedral_angle_3_deg 11.217 r_scangle_it 3.903 r_scbond_it 2.41 r_mcangle_it 1.698 r_angle_refined_deg 1.689 r_mcbond_it 0.995 r_angle_other_deg 0.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.521 r_dihedral_angle_4_deg 19.498 r_dihedral_angle_1_deg 13.458 r_dihedral_angle_3_deg 11.217 r_scangle_it 3.903 r_scbond_it 2.41 r_mcangle_it 1.698 r_angle_refined_deg 1.689 r_mcbond_it 0.995 r_angle_other_deg 0.868 r_mcbond_other 0.264 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2573 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling SHELX phasing SHELXD phasing SHELXE model building CRANK phasing