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Crystal structure of the first glutaredoxin domain of human glutaredoxin 3 (GLRX3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YAN PDB ENTRY 2YAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M BIS-TRIS PH 5.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.524 α = 90 b = 87.052 β = 90 c = 90.705 γ = 90
Symmetry Space Group P 2 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 6M 2011-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.84 19.62 97.8 0.13 11.4 6.3 23870 2.6 17.1
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 1.84 1.94 88.3 0.7 2.6 6
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 PDB ENTRY 2YAN 1.84 18.95 22530 1215 97.22 0.20241 0.19975 0.2042 0.24974 0.2509 RANDOM 14.264
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] -1.71 2.62 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.797 r_dihedral_angle_3_deg 12.512 r_dihedral_angle_4_deg 10.93 r_dihedral_angle_1_deg 5.587 r_angle_refined_deg 1.382 r_angle_other_deg 0.872 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.797 r_dihedral_angle_3_deg 12.512 r_dihedral_angle_4_deg 10.93 r_dihedral_angle_1_deg 5.587 r_angle_refined_deg 1.382 r_angle_other_deg 0.872 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing