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PTP1B with the catalytic cysteine oxidized to sulfonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HNP PDB ENTRY 2HNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5, 12%PEG, 0.2M MGCL2,CRYSTALS WERE SOAKED OVERNIGHT IN 100 MICROMOLAR PERVANADATE PRIOR TO DATA COLLECTION
Crystal Properties Matthews coefficient Solvent content 3.27 62.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.365 α = 90 b = 88.365 β = 90 c = 104.764 γ = 120
Symmetry Space Group P 31 2 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 CCD MARRESEARCH YALE MIRRORS 2002-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.15 25 98.1 0.071 25.68 6.98 26299
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 2.15 2.2 96.7 0.332 3.97
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 PDB ENTRY 2HNP 2.15 76.7 24459 1305 98.1 0.184 0.182 0.186 0.217 0.1965 RANDOM 30.6
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] 0.43 0.21 0.43 -0.64
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.311 r_dihedral_angle_1_deg 6.141 r_scbond_it 3.883 r_mcangle_it 2.458 r_angle_refined_deg 1.989 r_mcbond_it 1.313 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.236 r_chiral_restr 0.154 r_xyhbond_nbd_refined 0.137
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.311 r_dihedral_angle_1_deg 6.141 r_scbond_it 3.883 r_mcangle_it 2.458 r_angle_refined_deg 1.989 r_mcbond_it 1.313 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.236 r_chiral_restr 0.154 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.131 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2292 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing