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Crystal structure of Human Glutaredoxin 2 complexed with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CQ9 PDB ENTRY 2CQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 0.1 M citrate, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.201 α = 90 b = 60.201 β = 90 c = 67.958 γ = 120
Symmetry Space Group P 32 2 1
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 2005-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9184 SLS X10SA
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 2.05 41.38 100 0.115 13.5 5.9 9322 9322 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 100 2.5 5.8 7834
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 PDB ENTRY 2CQ9 2.05 41.38 8589 8589 448 97.11 0.192 0.19238 0.19045 0.1946 0.2309 0.1943 RANDOM 23.02
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] 0.87 0.43 0.87 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.601 r_dihedral_angle_4_deg 18.745 r_dihedral_angle_3_deg 13.074 r_scangle_it 7.237 r_dihedral_angle_1_deg 6.543 r_scbond_it 6.23 r_mcangle_it 3.777 r_mcbond_it 2.754 r_angle_refined_deg 1.502 r_angle_other_deg 1.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.601 r_dihedral_angle_4_deg 18.745 r_dihedral_angle_3_deg 13.074 r_scangle_it 7.237 r_dihedral_angle_1_deg 6.543 r_scbond_it 6.23 r_mcangle_it 3.777 r_mcbond_it 2.754 r_angle_refined_deg 1.502 r_angle_other_deg 1.005 r_mcbond_other 0.75 r_symmetry_vdw_other 0.372 r_nbd_refined 0.19 r_nbd_other 0.186 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.142 r_nbtor_other 0.088 r_chiral_restr 0.082 r_bond_refined_d 0.017 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_vdw_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 784 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing