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Human PTPRZ D1 domain complexed with NAZ2329
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 10%(w/v) PEG8000, 20%(v/v) ethylene glycol, 30mM sodium fluoride, 30mM sodium bromide, 30mM sodium iodide. NAZ2329 was soaked into the crystal.
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.776 α = 90 b = 72.306 β = 90 c = 90.796 γ = 90
Symmetry Space Group P 21 21 21
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 2015-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.53 100 87.2 0.03 30.6 4.5 10798
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 5AWX 2.53 45.4 9992 536 84.97 0.21476 0.21029 0.2057 0.29689 0.2908 RANDOM 39.25
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] -29.55 11.65 17.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_4_deg 18.988 r_dihedral_angle_3_deg 18.407 r_dihedral_angle_1_deg 7.877 r_long_range_B_refined 2.377 r_long_range_B_other 2.376 r_angle_refined_deg 1.894 r_mcangle_it 1.261 r_mcangle_other 1.261 r_angle_other_deg 1.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_4_deg 18.988 r_dihedral_angle_3_deg 18.407 r_dihedral_angle_1_deg 7.877 r_long_range_B_refined 2.377 r_long_range_B_other 2.376 r_angle_refined_deg 1.894 r_mcangle_it 1.261 r_mcangle_other 1.261 r_angle_other_deg 1.083 r_scangle_other 0.955 r_mcbond_it 0.709 r_mcbond_other 0.709 r_scbond_other 0.529 r_scbond_it 0.528 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2276 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing