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Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Orthorhombic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V2G PDB ENTRY 2V2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 RESERVOIR : BIS TRIS 0.1 M PH 5.5 , PEG 3350 25%(W/V). DTT 0.001 M DROP 1UL PROTEIN AND 1 UL RESERVOIR
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.11 α = 90 b = 111.156 β = 90 c = 229.8 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 MARRESEARCH TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING 2006-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.4 15 99 0.06 15.2 3.7 77362
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 2.4 2.5 96.9 0.42 3.3 3.4
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 2V2G 2.4 15 72061 3823 97.8 0.18 0.177 0.1797 0.239 0.2377 RANDOM 34.25
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] -0.04 0.07 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_3_deg 17.645 r_dihedral_angle_4_deg 17.622 r_dihedral_angle_1_deg 6.791 r_scangle_it 2.607 r_scbond_it 1.863 r_angle_refined_deg 1.737 r_mcangle_it 1.051 r_angle_other_deg 1.033 r_mcbond_it 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_3_deg 17.645 r_dihedral_angle_4_deg 17.622 r_dihedral_angle_1_deg 6.791 r_scangle_it 2.607 r_scbond_it 1.863 r_angle_refined_deg 1.737 r_mcangle_it 1.051 r_angle_other_deg 1.033 r_mcbond_it 0.802 r_symmetry_vdw_refined 0.24 r_symmetry_hbond_refined 0.226 r_symmetry_vdw_other 0.21 r_nbd_refined 0.205 r_nbd_other 0.201 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.097 r_nbtor_other 0.089 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_mcbond_other r_mcangle_other r_scbond_other 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 13593 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing