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Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.5 10% PEG 20k, 20% PEG MME 550, 0.1M bicine/Tris pH8.5, 0.03M sodium nitrate, 0.03M disodium hydrogen phosphate, 0.03M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.3 α = 90 b = 122.16 β = 109.79 c = 98.61 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2012-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9200 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 92.79 99.8 10.7 11.6 52662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 99.3 1.6 7.1
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 FREE R-VALUE 2YD4 2.5 92.79 49976 2676 99.86 0.21055 0.20858 0.24701 0.2245 RANDOM 56.72
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] -1.77 -0.38 -0.05 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 16.63 r_dihedral_angle_3_deg 14.794 r_dihedral_angle_1_deg 6.116 r_long_range_B_refined 4.568 r_long_range_B_other 4.528 r_scangle_other 2.924 r_mcangle_it 2.272 r_mcangle_other 2.272 r_scbond_it 1.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.603 r_dihedral_angle_4_deg 16.63 r_dihedral_angle_3_deg 14.794 r_dihedral_angle_1_deg 6.116 r_long_range_B_refined 4.568 r_long_range_B_other 4.528 r_scangle_other 2.924 r_mcangle_it 2.272 r_mcangle_other 2.272 r_scbond_it 1.811 r_scbond_other 1.807 r_mcbond_it 1.378 r_mcbond_other 1.378 r_angle_refined_deg 1.243 r_angle_other_deg 0.715 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8536 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing