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Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Monoclinic form 2
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 0.1M PH 5.5, PEG3350 25%(M/V), DTT 0.001M, AMMONIUM SULFATE 0.1M DROP 1UL PROTEIN AND 1 UL RESERVOIR
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.261 α = 90 b = 83.034 β = 116.72 c = 107.444 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MARRESEARCH MIRROR 1, FLAT PRE-MIRROR, MIRROR 2, BENT, VERTICALLY FOCUSSING 2006-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 20 95.8 0.11 8.9 3.1 65352
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 2.1 85.8 0.44 3 3
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 19.83 62040 3307 96.4 0.195 0.192 0.1935 0.26 0.262 RANDOM 16.75
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.305 r_dihedral_angle_3_deg 16.242 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_1_deg 6.573 r_scangle_it 4.141 r_scbond_it 2.862 r_angle_refined_deg 1.864 r_mcangle_it 1.698 r_mcbond_it 1.128 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.305 r_dihedral_angle_3_deg 16.242 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_1_deg 6.573 r_scangle_it 4.141 r_scbond_it 2.862 r_angle_refined_deg 1.864 r_mcangle_it 1.698 r_mcbond_it 1.128 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.243 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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_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 6791 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing