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Complex structure of Norrin with human Frizzled 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 200 mM ammonium sulfate, 100 mM sodium cacodylate trihydrate (pH 6.5), 15% w/v polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 3.62 66.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.291 α = 90 b = 150.589 β = 90 c = 92.32 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315r 2015-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.8 50 90.5 0.264 0.28 0.117 3.5 5.9 18303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.91 65.2 0.923 0.526 0.923 3.3 1084
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 4MY2 3.8 50 17383 889 89.49 0.2639 0.2615 0.2633 0.3105 0.3043 RANDOM 112.326
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] -0.11 -0.93 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.752 r_dihedral_angle_3_deg 12.859 r_dihedral_angle_4_deg 10.322 r_dihedral_angle_1_deg 4.157 r_mcangle_it 2.652 r_mcbond_it 1.453 r_mcbond_other 1.453 r_angle_refined_deg 0.77 r_angle_other_deg 0.661 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.752 r_dihedral_angle_3_deg 12.859 r_dihedral_angle_4_deg 10.322 r_dihedral_angle_1_deg 4.157 r_mcangle_it 2.652 r_mcbond_it 1.453 r_mcbond_other 1.453 r_angle_refined_deg 0.77 r_angle_other_deg 0.661 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9171 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing