9NK0 | pdb_00009nk0

Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum (apo)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52932:1 protein (20mM bistris pH 7.2, 200mM KCl, 1mM MnCl2, 5% glycerol) to condition (30% w/v PEG 5000 MME, 100 mM MES/ Sodium hydroxide pH 6.5, 200 mM ammonium sulfate)
Crystal Properties
Matthews coefficientSolvent content
2.4850.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.083α = 90
b = 76.697β = 90
c = 80.594γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2024-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-10.987SSRLBL12-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.5238.3599.70.0250.0271466.628916
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)
11.521.5599.80.980.1060.570.99516.96.7

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 REPLACEMENTTHROUGHOUT1.5238.34828916150299.5390.1290.12670.12790.16480.165919.046
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]
-2.1070.221.887
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it18.394
r_lrange_other15.906
r_dihedral_angle_6_deg14.662
r_dihedral_angle_2_deg14.155
r_dihedral_angle_3_deg11.838
r_scangle_it11.826
r_scangle_other11.82
r_scbond_it8.396
r_scbond_other8.392
r_mcangle_other7.887
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it18.394
r_lrange_other15.906
r_dihedral_angle_6_deg14.662
r_dihedral_angle_2_deg14.155
r_dihedral_angle_3_deg11.838
r_scangle_it11.826
r_scangle_other11.82
r_scbond_it8.396
r_scbond_other8.392
r_mcangle_other7.887
r_mcangle_it7.88
r_dihedral_angle_1_deg6.911
r_mcbond_it5.513
r_mcbond_other5.513
r_rigid_bond_restr5.272
r_angle_refined_deg1.977
r_angle_other_deg0.805
r_nbd_refined0.247
r_symmetry_xyhbond_nbd_refined0.213
r_symmetry_nbd_refined0.189
r_xyhbond_nbd_refined0.174
r_nbtor_refined0.166
r_symmetry_nbd_other0.163
r_nbd_other0.123
r_chiral_restr0.104
r_symmetry_nbtor_other0.077
r_metal_ion_refined0.073
r_symmetry_xyhbond_nbd_other0.039
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1198
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing