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Crystal structure of soybean ascorbate peroxidase mutant W41A after exposure to a high dose of x-rays
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GGN PDB ENTRY 2GGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 pH 8.3
Crystal Properties Matthews coefficient Solvent content 1.97 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.002 α = 90 b = 82.002 β = 90 c = 75.57 γ = 90
Symmetry Space Group P 42 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 ADSC CCD 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.6 37.8 100 0.09 19.5 10.18 34661 3
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 1.6 1.69 100 0.66 3.1 9.89
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 2GGN 1.5 37.8 39733 2113 100 0.177 0.175 0.1721 0.209 0.207 RANDOM 15.68
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] -0.13 -0.13 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.673 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 11.239 r_dihedral_angle_1_deg 4.976 r_scangle_it 2.949 r_scbond_it 1.958 r_mcangle_it 1.348 r_angle_refined_deg 1.152 r_mcbond_it 0.824 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.673 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 11.239 r_dihedral_angle_1_deg 4.976 r_scangle_it 2.949 r_scbond_it 1.958 r_mcangle_it 1.348 r_angle_refined_deg 1.152 r_mcbond_it 0.824 r_nbtor_refined 0.305 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 1874 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing