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Crystal structure of the phosphatase domains of human PTP SIGMA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 Protein(10mg/ml) was crystallized in (15% PEG3350,100mM Succinic Acid)., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.333 α = 90 b = 94.333 β = 90 c = 123.036 γ = 120
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 2005-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.81 25.76 99 0.093 0.093 6 9.3 55608
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) 1.81 1.91 93.3 0.011 0.0115 0.6 6.9 7637
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 1LAR 2 24.67 41832 55608 2103 99.95 0.192 0.19199 0.19 0.1899 0.238 0.2368 RANDOM 28.698
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.674 r_dihedral_angle_4_deg 15.221 r_dihedral_angle_3_deg 13.789 r_dihedral_angle_1_deg 5.768 r_scangle_it 2.616 r_scbond_it 1.693 r_mcangle_it 1.228 r_angle_refined_deg 1.148 r_mcbond_it 0.736 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.674 r_dihedral_angle_4_deg 15.221 r_dihedral_angle_3_deg 13.789 r_dihedral_angle_1_deg 5.768 r_scangle_it 2.616 r_scbond_it 1.693 r_mcangle_it 1.228 r_angle_refined_deg 1.148 r_mcbond_it 0.736 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4648 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling