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Crystal structure of dithinonite reduced soybean ascorbate peroxidase mutant W41A.
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 2.06 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.78 α = 90 b = 81.78 β = 90 c = 75.244 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 2006-04-29 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 1.3 45.83 99.9 0.09 21.6 10.29 63112 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 1.3 1.39 100 0.45 4.3 10.4
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 2GGN 1.3 34.18 59870 3196 99.9 0.182 0.181 0.1783 0.199 0.1973 RANDOM 12.42
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.227 r_dihedral_angle_4_deg 17.781 r_dihedral_angle_3_deg 11.752 r_dihedral_angle_1_deg 4.97 r_scangle_it 2.439 r_scbond_it 1.597 r_mcangle_it 1.135 r_angle_refined_deg 1.117 r_mcbond_it 0.651 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.227 r_dihedral_angle_4_deg 17.781 r_dihedral_angle_3_deg 11.752 r_dihedral_angle_1_deg 4.97 r_scangle_it 2.439 r_scbond_it 1.597 r_mcangle_it 1.135 r_angle_refined_deg 1.117 r_mcbond_it 0.651 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.073 r_bond_refined_d 0.006 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 1862 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing