6F56

Mutant of Human N-myristoyltransferase with bound myristoyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293.15PEG 4000 22 % Sodium citrate 0.1 M Glycerol 2.5 %
Crystal Properties
Matthews coefficientSolvent content
2.2845.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.19α = 90
b = 159.13β = 90
c = 174.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2017-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

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
11.9487.49592.80.10.1190.0630.99811.36.5112254226.7375608735
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)
11.941.97472.20.8391.0030.5410.8012.15.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4C2Y1.940198766887.4951.34087675499112134551792.66506900260.2015326982320.1995502790570.23943828516834.4604115534
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
f_dihedral_angle_d17.6566551606
f_angle_d0.690587428121
f_chiral_restr0.0475250452296
f_plane_restr0.00417101209466
f_bond_d0.00323425617943
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12532
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms310

Software

Software
Software NamePurpose
autoPROCdata collection
PHASERphasing
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling