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CHARACTERIZATION OF HUMAN TRIOSEPHOSPHATE ISOMERASE S-NITROSYLATION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 283 0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.92 α = 90 b = 73.98 β = 90 c = 93.8 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 PIXEL DECTRIS PILATUS 2M 2017-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.04 58.09 95.2 0.126 0.145 0.068 0.919 8.2 4.7 27988
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 89.7 0.301 0.346 0.163 0.567 4.5
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 FOURIER SYNTHESIS THROUGHOUT 2JK2 2.04 58.09 26617 1327 94.51 0.20444 0.2018 0.2114 0.2563 0.263 RANDOM 18.081
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] -0.14 1.62 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.77 r_dihedral_angle_3_deg 13.125 r_dihedral_angle_4_deg 8.921 r_dihedral_angle_1_deg 5.949 r_long_range_B_refined 3.246 r_long_range_B_other 2.949 r_mcangle_it 1.305 r_mcangle_other 1.305 r_angle_refined_deg 1.283 r_scangle_other 1.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.77 r_dihedral_angle_3_deg 13.125 r_dihedral_angle_4_deg 8.921 r_dihedral_angle_1_deg 5.949 r_long_range_B_refined 3.246 r_long_range_B_other 2.949 r_mcangle_it 1.305 r_mcangle_other 1.305 r_angle_refined_deg 1.283 r_scangle_other 1.264 r_angle_other_deg 0.902 r_mcbond_it 0.756 r_mcbond_other 0.756 r_scbond_it 0.727 r_scbond_other 0.726 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 3708 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction REFMAC phasing