9O5M | pdb_00009o5m

Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to prenylated flavin mononucleotide in the P1 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherApo PhdC solved previously by our group, deposited as 9NK0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52931:2 condition (100 mM citric acid/NaOH pH 5.0, 20% w/v PEG 6K) to buffer (20 mM BisTris pH 7.2 200 mM KCl). Protein reconstituted with prFMN
Crystal Properties
Matthews coefficientSolvent content
2.3948.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.552α = 69.95
b = 60.19β = 85.032
c = 65.053γ = 65.414
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2024-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.976SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6251.585.40.040.0470.0240.99918.83.875219
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.621.6550.50.1810.210.1060.975.93.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.6251.49975118371285.3230.1690.1680.1680.19550.195521.655
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]
0.4-0.0780.614-0.2330.159-0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.088
r_dihedral_angle_3_deg12.51
r_dihedral_angle_2_deg9.909
r_lrange_it7.258
r_dihedral_angle_1_deg6.658
r_scangle_it5.884
r_scbond_it3.961
r_mcangle_it2.97
r_angle_refined_deg2.15
r_mcbond_it2.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.088
r_dihedral_angle_3_deg12.51
r_dihedral_angle_2_deg9.909
r_lrange_it7.258
r_dihedral_angle_1_deg6.658
r_scangle_it5.884
r_scbond_it3.961
r_mcangle_it2.97
r_angle_refined_deg2.15
r_mcbond_it2.082
r_nbtor_refined0.311
r_symmetry_nbd_refined0.223
r_nbd_refined0.212
r_symmetry_xyhbond_nbd_refined0.176
r_chiral_restr0.143
r_xyhbond_nbd_refined0.142
r_metal_ion_refined0.098
r_ncsr_local_group_10.085
r_ncsr_local_group_50.083
r_ncsr_local_group_40.077
r_ncsr_local_group_20.068
r_ncsr_local_group_60.068
r_ncsr_local_group_30.064
r_gen_planes_refined0.013
r_bond_refined_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4791
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building