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Crystal structure of Human PTPRZ D1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QCB
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
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.641 α = 90 b = 72.245 β = 90 c = 90.557 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 RAXIS IV++ 2013-04-17 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 1.86 31.4 99.5 0.039 45.9 7.6 29084
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 3QCB 1.86 31.4 29084 1547 99.45 0.18745 0.18563 0.1875 0.22094 0.2227 RANDOM 22.281
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] -2.27 -0.2 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_4_deg 12.545 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 5.803 r_long_range_B_other 5.622 r_scangle_other 3.743 r_scbond_it 2.436 r_scbond_other 2.436 r_mcangle_other 2.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_4_deg 12.545 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 5.803 r_long_range_B_other 5.622 r_scangle_other 3.743 r_scbond_it 2.436 r_scbond_other 2.436 r_mcangle_other 2.308 r_mcangle_it 2.307 r_angle_refined_deg 1.977 r_mcbond_it 1.651 r_mcbond_other 1.621 r_angle_other_deg 1.006 r_chiral_restr 0.164 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2280 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing