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Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BPB 5BPB,5BPU experimental model PDB 5BPU 5BPB,5BPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.1 M Tris, pH 8.0, 0.15 M NaCl, 8% PEG8000
Crystal Properties Matthews coefficient Solvent content 4.03 69.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.136 α = 90 b = 119.136 β = 90 c = 119.151 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS PILATUS 6M 2014-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 47.34 100 0.13 0.031 0.999 14.6 19.6 10503
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 3.18 100 2.46 0.548 0.149 1.6 20.6 1648
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5BPB,5BPU 3 47.34 9904 571 99.92 0.2175 0.2147 0.2676 0.2372 RANDOM 113.96
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 -1.5 -3 9.74
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.748 r_sphericity_bonded 22.406 r_mcangle_it 7.397 r_mcbond_it 5.283 r_mcbond_other 5.28 r_angle_refined_deg 1.181 r_rigid_bond_restr 1.08 r_angle_other_deg 0.935 r_chiral_restr 0.05 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.748 r_sphericity_bonded 22.406 r_mcangle_it 7.397 r_mcbond_it 5.283 r_mcbond_other 5.28 r_angle_refined_deg 1.181 r_rigid_bond_restr 1.08 r_angle_other_deg 0.935 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1759 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 83
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction