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Joint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: complex with thioNADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQ7 PDB ENTRY 2VQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 277 CRYSTALS WERE OBTAINED USING MICROBATCH TECHNIQUE UNDER 100% PARAFFIN OIL AT 4 C BY MIXING EQUAL VOLUMES OF 8 MG PROTEIN/ML IN 25 MM TRIS/HCL PH 8.0, 250 MM NACL, 1 MM NADP (OR ANALOGUE), AND 20% (W/V) PEG4000 IN 100 MM NA/HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 4.3 71.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.679 α = 90 b = 220.679 β = 90 c = 130.531 γ = 120
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.6 42 99.9 0.12 9.7 5 110842
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 2.6 2.74 100 0.41 3.7 4.9
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 2VQ7 2.6 41.15 105293 5537 99.94 0.21204 0.20997 0.2079 0.25188 0.2493 RANDOM 28.502
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] -1.57 -0.78 -1.57 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.223 r_dihedral_angle_3_deg 17.817 r_dihedral_angle_4_deg 14.904 r_dihedral_angle_1_deg 7.244 r_scangle_it 3.727 r_scbond_it 2.312 r_angle_refined_deg 2.009 r_mcangle_it 1.456 r_mcbond_it 0.742 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.223 r_dihedral_angle_3_deg 17.817 r_dihedral_angle_4_deg 14.904 r_dihedral_angle_1_deg 7.244 r_scangle_it 3.727 r_scbond_it 2.312 r_angle_refined_deg 2.009 r_mcangle_it 1.456 r_mcbond_it 0.742 r_chiral_restr 0.136 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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 14620 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 440
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing