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Structure of the mitochondrial 2-cys peroxiredoxin from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E2Y PDB ENTRY 1E2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2M AMMONIUM SULFATE, 0.1M BIS-TRIS 6.5, 25% PEG 3350, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.4 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.632 α = 90 b = 76.534 β = 113.34 c = 60.154 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 ADSC CCD MIRRORS 2005-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.78 55.22 100 0.09 13.45 3.61 41762 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 1.78 1.88 100 0.25 2.58 3.58
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 1E2Y 1.78 59.87 39652 2106 100 0.167 0.165 0.1651 0.204 0.2034 RANDOM 15.29
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] -0.46 -0.18 0.49 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.395 r_dihedral_angle_4_deg 14.293 r_dihedral_angle_3_deg 13.257 r_dihedral_angle_1_deg 5.274 r_scangle_it 4.702 r_scbond_it 3.246 r_mcangle_it 1.9 r_angle_refined_deg 1.505 r_mcbond_it 1.15 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.395 r_dihedral_angle_4_deg 14.293 r_dihedral_angle_3_deg 13.257 r_dihedral_angle_1_deg 5.274 r_scangle_it 4.702 r_scbond_it 3.246 r_mcangle_it 1.9 r_angle_refined_deg 1.505 r_mcbond_it 1.15 r_nbtor_refined 0.313 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 2658 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing