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The structure of dimeric human glutaredoxin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.6M MgSO4, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.754 α = 90 b = 111.754 β = 90 c = 51.647 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 MARRESEARCH 2006-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.976 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 96.674 91.7 0.065 0.065 7.3 3.9 26417 26417 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 87.1 0.416 0.416 1.8 3.1 3637
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 2fls 1.9 96.67 26404 25063 1341 90.38 0.151 0.15088 0.14939 0.1899 0.17829 0.2145 RANDOM 26.188
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] 0.8 0.4 0.8 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.085 r_sphericity_bonded 15.612 r_dihedral_angle_3_deg 12.937 r_dihedral_angle_4_deg 11.432 r_scangle_it 9.199 r_scbond_it 6.98 r_rigid_bond_restr 6.261 r_dihedral_angle_1_deg 5.975 r_mcangle_it 4.404 r_mcbond_it 3.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.085 r_sphericity_bonded 15.612 r_dihedral_angle_3_deg 12.937 r_dihedral_angle_4_deg 11.432 r_scangle_it 9.199 r_scbond_it 6.98 r_rigid_bond_restr 6.261 r_dihedral_angle_1_deg 5.975 r_mcangle_it 4.404 r_mcbond_it 3.467 r_angle_refined_deg 1.448 r_mcbond_other 1.046 r_angle_other_deg 0.971 r_nbd_refined 0.201 r_nbd_other 0.179 r_nbtor_refined 0.173 r_symmetry_vdw_other 0.167 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.122 r_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1755 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 44
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling