7KL8

Structure of F420 binding protein Rv1558 from Mycobacterium tuberculosis with F420 bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R5R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2920.1 M Sodium citrate pH 5.8, 0.5 M Ammonium sulfate, 1 M Lithium sulfate, and 3 % Glycerol (v/v)
Crystal Properties
Matthews coefficientSolvent content
6.4780.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.544α = 90
b = 169.544β = 90
c = 169.544γ = 90
Symmetry
Space GroupP 43 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953719973564Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.46948.9999.70.1870.028128.578.530473
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4692.55897.545.9630.9450.4161.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3R5R2.46948.9928938159599.80.201060.200030.22012RANDOM83.23
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.573
r_dihedral_angle_3_deg14.91
r_dihedral_angle_4_deg14.244
r_long_range_B_other7.481
r_long_range_B_refined7.466
r_dihedral_angle_1_deg5.49
r_scangle_other4.637
r_mcangle_it3.276
r_mcangle_other3.275
r_scbond_it3.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.573
r_dihedral_angle_3_deg14.91
r_dihedral_angle_4_deg14.244
r_long_range_B_other7.481
r_long_range_B_refined7.466
r_dihedral_angle_1_deg5.49
r_scangle_other4.637
r_mcangle_it3.276
r_mcangle_other3.275
r_scbond_it3.225
r_scbond_other2.991
r_mcbond_it2.095
r_mcbond_other2.095
r_angle_refined_deg1.248
r_angle_other_deg0.996
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2216
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing