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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 2YOR PDB ENTRY 2YOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.15 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, 15% PEG4000, 15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.495 α = 90 b = 75.698 β = 90 c = 104.43 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 2011-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.83 50 99.7 0.06 24.27 7.3 46573 -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 1.83 1.94 98.2 0.46 4.06 7.3
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 2YOR 1.83 44.77 44243 2329 99.72 0.15633 0.15453 0.1553 0.18975 0.1899 RANDOM 23.834
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] -1.37 -0.75 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.976 r_dihedral_angle_4_deg 19.679 r_dihedral_angle_3_deg 13.464 r_dihedral_angle_1_deg 7.076 r_scbond_it 4.254 r_mcangle_it 3.603 r_mcbond_it 2.969 r_angle_refined_deg 1.47 r_chiral_restr 0.105 r_gen_planes_refined 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.976 r_dihedral_angle_4_deg 19.679 r_dihedral_angle_3_deg 13.464 r_dihedral_angle_1_deg 7.076 r_scbond_it 4.254 r_mcangle_it 3.603 r_mcbond_it 2.969 r_angle_refined_deg 1.47 r_chiral_restr 0.105 r_gen_planes_refined 0.016 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 3602 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing