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Crystal structure of the D1 domain of PTPRN2 (IA2beta)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1Y PDB entry 2I1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Na/KPO4, 0.1 M Bis-tris-propane pH 6.5, 20.0% PEG 3350, 10.0% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.541 α = 90 b = 136.555 β = 90 c = 35.752 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 MARMOSAIC 225 mm CCD 2007-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99990 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 59.23 99.5 0.139 0.139 9.1 3.5 23096 23096
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.7 0.465 0.465 1.9 3.5 11455
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2I1Y 2.5 59.23 21905 21905 1187 99.14 0.2389 0.2389 0.23634 0.2425 0.28601 0.2912 RANDOM 31.042
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] 1.7 -2.97 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_3_deg 15.183 r_dihedral_angle_4_deg 12.526 r_dihedral_angle_1_deg 6.512 r_scangle_it 1.556 r_angle_refined_deg 1.31 r_scbond_it 1.069 r_angle_other_deg 0.882 r_mcangle_it 0.789 r_mcbond_it 0.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_3_deg 15.183 r_dihedral_angle_4_deg 12.526 r_dihedral_angle_1_deg 6.512 r_scangle_it 1.556 r_angle_refined_deg 1.31 r_scbond_it 1.069 r_angle_other_deg 0.882 r_mcangle_it 0.789 r_mcbond_it 0.467 r_symmetry_vdw_other 0.291 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.218 r_nbd_other 0.188 r_nbtor_refined 0.188 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.15 r_mcbond_other 0.09 r_nbtor_other 0.086 r_chiral_restr 0.071 r_xyhbond_nbd_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4413 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing