2XLR

Joint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: Asn78Asp mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VQ7PDB ENTRY 2VQ7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.5277CRYSTALS 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 coefficientSolvent content
4.7474.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 214.059α = 90
b = 214.059β = 90
c = 152.811γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.5541000.18.93.7129218
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.71000.52.93.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VQ72.5553.51122681642599.910.21540.21390.24423RANDOM41.762
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]
0.420.210.42-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_dihedral_angle_4_deg21.082
r_dihedral_angle_3_deg20.136
r_dihedral_angle_1_deg5.857
r_scangle_it4.743
r_scbond_it2.92
r_angle_refined_deg1.952
r_mcangle_it1.862
r_mcbond_it0.907
r_chiral_restr0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_dihedral_angle_4_deg21.082
r_dihedral_angle_3_deg20.136
r_dihedral_angle_1_deg5.857
r_scangle_it4.743
r_scbond_it2.92
r_angle_refined_deg1.952
r_mcangle_it1.862
r_mcbond_it0.907
r_chiral_restr0.131
r_bond_refined_d0.024
r_gen_planes_refined0.01
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_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 AtomsNumber
Protein Atoms14671
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms404

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing