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Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FUJ PDB ENTRY 5FUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN WAS CRYSTALLIZED IN 18% PEG 4000, 15% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.17 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.01 α = 90 b = 76.67 β = 90 c = 120.8 γ = 90
Symmetry Space Group P 21 21 21
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 2013-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.55 50 98.5 0.04 16.67 3.3 79844 -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 1.55 1.65 92.6 0.37 2.1 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 5FUJ 1.55 32.36 75966 3999 98.28 0.15628 0.15485 0.1684 0.18297 0.1947 RANDOM 23.484
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] 2.02 -1.25 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 12.674 r_dihedral_angle_1_deg 6.38 r_scbond_it 3.062 r_mcangle_it 2.81 r_angle_refined_deg 2.061 r_mcbond_it 1.961 r_mcbond_other 1.961 r_angle_other_deg 0.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.19 r_dihedral_angle_4_deg 16.838 r_dihedral_angle_3_deg 12.674 r_dihedral_angle_1_deg 6.38 r_scbond_it 3.062 r_mcangle_it 2.81 r_angle_refined_deg 2.061 r_mcbond_it 1.961 r_mcbond_other 1.961 r_angle_other_deg 0.968 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.014 r_gen_planes_other 0.014 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 3566 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 366
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing