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Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 3-[(3,4-dichlorobenzyl)sulfanyl]-N-(methylsulfonyl)thiophene-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QCD PDB ENTRY 3QCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 pH 7.0, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.55 65.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.8 α = 90 b = 75.8 β = 90 c = 152.9 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE RIGAKU RAXIS IV++ VARIMAX HR 2006-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 2.4 50 99.8 0.186 9 7.9 20534 60.2
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 2.4 2.49 100 0.651 3.5 7.9
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 (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 3QCD 2.4 33.96 20387 20387 599 99.1 0.241 0.24 0.2427 0.272 0.2787 RANDOM 52.1
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] 9.02 5.02 9.02 -18.04
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.96 c_mcangle_it 2.5 c_scbond_it 1.97 c_mcbond_it 1.48 c_angle_deg 1.4 c_improper_angle_d 0.64 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.96 c_mcangle_it 2.5 c_scbond_it 1.97 c_mcbond_it 1.48 c_angle_deg 1.4 c_improper_angle_d 0.64 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2277 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing CNX refinement