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SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE STABILIZATION: COMPLEX WITH NADP and MES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YLR PDB ENTRY 2YLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 BY VAPOR-DIFFUSION AT 4 DEGREES C USING 1-3 MICROL OF PROTEIN SOLUTIONS (18 MG/ML IN 0.5 MICROM FAD AND 4 MM NADP, 50 MM TRIS/HCL PH 7.5) MIXED WITH EQUAL VOLUMES OF RESERVOIR CONTAINING 40% W/V PEG4000, 100 MM MES/HCL PH 6.5, AND 100 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.93 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.35 α = 90 b = 107.35 β = 90 c = 107.7 γ = 120
Symmetry Space Group P 32 2 1
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 QUANTUM 210 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 2.65 30 99.3 0.11 9.9 3.6 21047
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 2.65 2.8 98.8 0.52 2.6 3.7
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 2YLR 2.65 48.04 19992 1020 98.71 0.19594 0.19262 0.1919 0.26111 0.2562 RANDOM 41.575
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] 1.52 0.76 1.52 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.457 r_dihedral_angle_3_deg 18.983 r_dihedral_angle_4_deg 17.637 r_dihedral_angle_1_deg 6.533 r_scangle_it 3.169 r_scbond_it 1.929 r_angle_refined_deg 1.679 r_mcangle_it 1.242 r_mcbond_it 0.654 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.457 r_dihedral_angle_3_deg 18.983 r_dihedral_angle_4_deg 17.637 r_dihedral_angle_1_deg 6.533 r_scangle_it 3.169 r_scbond_it 1.929 r_angle_refined_deg 1.679 r_mcangle_it 1.242 r_mcbond_it 0.654 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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_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 4223 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing