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HUMAN PEROXIREDOXIN 5, C47S MUTANT
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 5.3 PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE BUFFER PH 5.3, 0.2 M POTASSIUM SODIUM TARTRATE, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE
Crystal Properties Matthews coefficient Solvent content 3.4 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.646 α = 90 b = 65.646 β = 90 c = 122.043 γ = 90
Symmetry Space Group P 41 21 2
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 BENT MIRROR 2001-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 1.7 37 99.8 0.053 32 6.1 30149
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 1.7 1.74 100 0.292 5.5 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HD2 1.7 40 28558 1527 99.8 0.147 0.146 0.169 0.2116 RANDOM 15.15
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] 0.47 0.47 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.913 r_scangle_it 4.045 r_scbond_it 2.437 r_angle_refined_deg 1.63 r_mcangle_it 1.49 r_angle_other_deg 0.842 r_mcbond_it 0.822 r_nbd_other 0.26 r_nbd_refined 0.219 r_symmetry_vdw_other 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.913 r_scangle_it 4.045 r_scbond_it 2.437 r_angle_refined_deg 1.63 r_mcangle_it 1.49 r_angle_other_deg 0.842 r_mcbond_it 0.822 r_nbd_other 0.26 r_nbd_refined 0.219 r_symmetry_vdw_other 0.213 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.108 r_nbtor_other 0.093 r_bond_refined_d 0.019 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 1196 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling