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Crystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PN8 PDB ENTRY 2PN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 10% polyethylene glycol monomethyl ether 5000, 0.1M HEPES-NaOH, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.121 α = 90 b = 195.998 β = 105.23 c = 51.74 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 CCD RAYONIX MX-225 2009-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9999 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 98.9 0.066 0.066 12.4 3.5 108135 -3 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 94.2 0.214 0.214 5.2 3.2
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 2PN8 1.9 37.98 102513 5372 98.77 0.19682 0.19561 0.1995 0.21976 0.2244 RANDOM 33.509
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] -0.81 -1.97 -2.52 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.303 r_dihedral_angle_3_deg 13.478 r_dihedral_angle_4_deg 9.789 r_dihedral_angle_1_deg 5.616 r_scangle_it 2.814 r_scbond_it 1.648 r_angle_refined_deg 1.281 r_mcangle_it 1.037 r_mcbond_it 0.546 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.303 r_dihedral_angle_3_deg 13.478 r_dihedral_angle_4_deg 9.789 r_dihedral_angle_1_deg 5.616 r_scangle_it 2.814 r_scbond_it 1.648 r_angle_refined_deg 1.281 r_mcangle_it 1.037 r_mcbond_it 0.546 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7784 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 30
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling