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Crystal structure of poplar glutaredoxin S12 in complex with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FLS PDB ENTRY 2FLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7.5 293.15 0.1 M Na HEPES (pH 7.5) and 20 % PEG 8000, microbatch under oil, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.09 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.032 α = 90 b = 47.265 β = 90 c = 55.62 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 CCD MAR CCD 165 mm 2007-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8150 EMBL/DESY, HAMBURG X11
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 1.7 50 99.7 0.045 13.4 4.5 11857
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) 1.7 1.73 95 0.24 2.3 4.2
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 (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 2FLS 1.7 31.94 11234 11233 564 99.26 0.19424 0.19201 0.1904 0.23761 0.2356 RANDOM 20.446
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] -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.794 r_dihedral_angle_3_deg 14.217 r_dihedral_angle_4_deg 12.609 r_dihedral_angle_1_deg 5.52 r_scangle_it 3.844 r_scbond_it 2.479 r_angle_refined_deg 1.397 r_mcangle_it 1.379 r_mcbond_it 0.857 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.794 r_dihedral_angle_3_deg 14.217 r_dihedral_angle_4_deg 12.609 r_dihedral_angle_1_deg 5.52 r_scangle_it 3.844 r_scbond_it 2.479 r_angle_refined_deg 1.397 r_mcangle_it 1.379 r_mcbond_it 0.857 r_nbtor_refined 0.303 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 819 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling