7OUJ

Crystal structure of the flavoprotein monooxygenase RubL from rubromycin biosynthesis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IHG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529520 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA pH 7.5 buffer system, 12.5% PEG 4000 and 20% 1,2,6-Hexanetriol
Crystal Properties
Matthews coefficientSolvent content
2.3447.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.323α = 90
b = 57.514β = 95.183
c = 122.379γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.5746.08940.0460.999.42.470014
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.660.550.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3IHG1.57337.77870008367394.0340.1840.1830.209527.196
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]
0.061-0.0020.051-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.758
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg12.73
r_dihedral_angle_1_deg6.289
r_lrange_it6.225
r_lrange_other6.201
r_scangle_it5.225
r_scangle_other5.225
r_scbond_it3.524
r_scbond_other3.523
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.758
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg12.73
r_dihedral_angle_1_deg6.289
r_lrange_it6.225
r_lrange_other6.201
r_scangle_it5.225
r_scangle_other5.225
r_scbond_it3.524
r_scbond_other3.523
r_mcangle_it3.184
r_mcangle_other3.183
r_mcbond_it2.275
r_mcbond_other2.275
r_angle_refined_deg1.702
r_angle_other_deg1.511
r_symmetry_nbd_refined0.291
r_nbd_other0.225
r_nbd_refined0.21
r_symmetry_xyhbond_nbd_refined0.209
r_symmetry_nbd_other0.183
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.127
r_chiral_restr0.085
r_symmetry_nbtor_other0.083
r_chiral_restr_other0.053
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3974
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing