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Crystal structure of the six N-terminal domains of human receptor protein tyrosine phosphatase sigma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YD3 2YD3, 2YD4, 2YD9, 2DJU experimental model PDB 2YD4 2YD3, 2YD4, 2YD9, 2DJU experimental model PDB 2YD9 2YD3, 2YD4, 2YD9, 2DJU experimental model PDB 2DJU 2YD3, 2YD4, 2YD9, 2DJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.5 10 % PEG 400, 0.01 M magnesium chloride, 0.1 M potassium chloride, 0.05 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 5.87 79.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.78 α = 90 b = 198.78 β = 90 c = 132.4 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 CCD ADSC QUANTUM 315r 2008-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9788 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.15 99.4 95.6 0.078 17.8 7.6 25619
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.23 96.1 0.991 2.1 7.5
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 2YD3, 2YD4, 2YD9, 2DJU 3.15 172.15 24310 1309 94.29 0.23562 0.23406 0.2359 0.26497 0.2626 RANDOM 120.828
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] 0.7 0.35 0.7 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.678 r_dihedral_angle_3_deg 14.843 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_1_deg 5.945 r_long_range_B_refined 4.515 r_long_range_B_other 4.515 r_mcangle_it 2.909 r_mcangle_other 2.909 r_scangle_other 2.525 r_mcbond_other 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.678 r_dihedral_angle_3_deg 14.843 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_1_deg 5.945 r_long_range_B_refined 4.515 r_long_range_B_other 4.515 r_mcangle_it 2.909 r_mcangle_other 2.909 r_scangle_other 2.525 r_mcbond_other 1.658 r_mcbond_it 1.657 r_scbond_it 1.395 r_scbond_other 1.395 r_angle_refined_deg 1.008 r_angle_other_deg 0.667 r_chiral_restr 0.06 r_bond_refined_d 0.005 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 4380 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing