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Crystal structure of the PTPRJ inactivating mutant C1239S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CFV pdb entry 2CFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.01M NiCl2, 0.1M TRIS, pH 8.5, 1M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.521 α = 90 b = 88.521 β = 90 c = 118.95 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 MARMOSAIC 225 mm CCD 2006-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.3 46.98 99.2 0.089 3.3 15274
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 2.3 2.42 95 0.387 2.7
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 2CFV 2.3 46.98 14581 14581 738 99.15 0.18399 0.18399 0.18179 0.182 0.2275 0.2269 RANDOM 22.442
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] 0.31 0.16 0.31 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.257 r_dihedral_angle_4_deg 16.095 r_dihedral_angle_3_deg 14.494 r_dihedral_angle_1_deg 6.569 r_scangle_it 1.901 r_scbond_it 1.391 r_angle_other_deg 1.314 r_angle_refined_deg 1.291 r_mcangle_it 0.978 r_mcbond_it 0.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.257 r_dihedral_angle_4_deg 16.095 r_dihedral_angle_3_deg 14.494 r_dihedral_angle_1_deg 6.569 r_scangle_it 1.901 r_scbond_it 1.391 r_angle_other_deg 1.314 r_angle_refined_deg 1.291 r_mcangle_it 0.978 r_mcbond_it 0.596 r_nbd_refined 0.199 r_nbd_other 0.198 r_symmetry_vdw_refined 0.18 r_nbtor_refined 0.175 r_symmetry_vdw_other 0.173 r_xyhbond_nbd_refined 0.147 r_mcbond_other 0.107 r_nbtor_other 0.087 r_symmetry_hbond_refined 0.078 r_chiral_restr 0.077 r_metal_ion_refined 0.042 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 2380 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling