9NK3 | pdb_00009nk3

Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium fortuitum (apo)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherInitial model was wt apo PhdC solved by our group (deposition in progress)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52931:1 crystallization condition (0.2M ammonium acetate, 0.1M HEPES/NaOH pH 7.5, 45% v/v MPD) to buffer (20 mM BisTris pH 7.2 200 mM KCl 1mM MnCl2).
Crystal Properties
Matthews coefficientSolvent content
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.801α = 90
b = 75.605β = 90
c = 80.895γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE CdTe 16M2024-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.729MAX IVBioMAX

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
11.3255.2483.90.0590.0630.020.99918.88.636263
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)
11.321.3450.70.4410.5210.2690.7672.53.4

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-VALUE1.3248.13436263175283.540.1220.12040.12040.14560.145619.124
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]
-2.0652.447-0.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.114
r_lrange_it18.026
r_lrange_other17.152
r_dihedral_angle_6_deg15.368
r_scangle_it14.558
r_scangle_other14.55
r_dihedral_angle_3_deg11.318
r_scbond_it10.461
r_scbond_other10.455
r_mcangle_other8.542
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.114
r_lrange_it18.026
r_lrange_other17.152
r_dihedral_angle_6_deg15.368
r_scangle_it14.558
r_scangle_other14.55
r_dihedral_angle_3_deg11.318
r_scbond_it10.461
r_scbond_other10.455
r_mcangle_other8.542
r_mcangle_it8.513
r_dihedral_angle_1_deg6.305
r_mcbond_it6.19
r_mcbond_other6.189
r_rigid_bond_restr5.354
r_angle_refined_deg2.137
r_angle_other_deg0.75
r_symmetry_nbd_refined0.423
r_nbd_other0.292
r_nbd_refined0.227
r_xyhbond_nbd_refined0.197
r_symmetry_nbd_other0.185
r_nbtor_refined0.175
r_symmetry_xyhbond_nbd_refined0.11
r_chiral_restr0.109
r_symmetry_nbtor_other0.088
r_metal_ion_refined0.065
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_symmetry_xyhbond_nbd_other0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1183
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
Cootmodel building