6H6V

Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with FMN


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.1 M Tris/BICINE buffer pH 8.5, 20% v/v ethylene glycol and 10% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.7655.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.91α = 90
b = 139.25β = 93.74
c = 136.88γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6674.299.80.14419.83.8343818
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.662.7399.81.1030.51.63.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.6674.286650431199.780.200970.19920.23599RANDOM55.86
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]
3.24-0.68-3.190.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.679
r_dihedral_angle_4_deg19.191
r_dihedral_angle_3_deg17.685
r_long_range_B_refined9.974
r_long_range_B_other9.974
r_scangle_other6.956
r_dihedral_angle_1_deg6.23
r_mcangle_it5.891
r_mcangle_other5.891
r_scbond_other4.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.679
r_dihedral_angle_4_deg19.191
r_dihedral_angle_3_deg17.685
r_long_range_B_refined9.974
r_long_range_B_other9.974
r_scangle_other6.956
r_dihedral_angle_1_deg6.23
r_mcangle_it5.891
r_mcangle_other5.891
r_scbond_other4.431
r_scbond_it4.43
r_mcbond_it3.74
r_mcbond_other3.738
r_angle_refined_deg1.58
r_angle_other_deg0.968
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20433
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms204

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MLPHAREphasing