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Crystal structure of peroxiredoxin 5 from Arenicola Marina
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HD2 PDB ENTRY 1HD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PEG 4000 29%(W/V), DTT 0.001 M
Crystal Properties Matthews coefficient Solvent content 1.98 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.21 α = 90 b = 112.07 β = 97.35 c = 68.91 γ = 90
Symmetry Space Group P 1 21 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 ADSC CCD SECOND CRYSTAL SAGITALLY BENT 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 1.75 34.17 95.6 0.05 17.7 3.7 51140 24.2
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 1.75 1.79 82.5 0.27 4.4 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 1HD2 1.75 68.36 48544 2596 95.6 0.165 0.163 0.2071 0.213 0.2484 RANDOM 20.57
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] 0.17 0.43 1.1 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.739 r_dihedral_angle_3_deg 14.203 r_dihedral_angle_4_deg 10.358 r_dihedral_angle_1_deg 6.403 r_scangle_it 3.773 r_scbond_it 2.529 r_angle_refined_deg 1.676 r_mcangle_it 1.438 r_angle_other_deg 0.96 r_mcbond_it 0.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.739 r_dihedral_angle_3_deg 14.203 r_dihedral_angle_4_deg 10.358 r_dihedral_angle_1_deg 6.403 r_scangle_it 3.773 r_scbond_it 2.529 r_angle_refined_deg 1.676 r_mcangle_it 1.438 r_angle_other_deg 0.96 r_mcbond_it 0.883 r_mcbond_other 0.301 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 4620 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing