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Crystal structure of poplar glutaredoxin S12 in complex with glutathione and beta-mercaptoethanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FZ9 Poplar GrxS12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7.5 293.15 0.1M Na HEPES (pH 7.5), 25% PEG 1000, microbatch under oil, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.05 40.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.829 α = 90 b = 46.816 β = 90 c = 55.36 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 2006-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8063 EMBL/DESY, HAMBURG X13
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 1.8 50 99.6 0.048 23.3 6.7 10048 2 2
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) 1.8 1.86 100 0.11 16.9 6.8
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 Poplar GrxS12 1.8 30 9300 470 99.61 0.17099 0.16908 0.1683 0.20995 0.2087 RANDOM 16.353
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] -0.05 0.11 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.538 r_dihedral_angle_4_deg 12.897 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_1_deg 5.684 r_scangle_it 3.796 r_scbond_it 2.383 r_angle_refined_deg 1.331 r_mcangle_it 1.244 r_mcbond_it 0.762 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.538 r_dihedral_angle_4_deg 12.897 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_1_deg 5.684 r_scangle_it 3.796 r_scbond_it 2.383 r_angle_refined_deg 1.331 r_mcangle_it 1.244 r_mcbond_it 0.762 r_nbtor_refined 0.306 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.085 r_bond_refined_d 0.011 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 204 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling