3H5Z

Crystal Structure of Leishmania major N-myristoyltransferase with bound myristoyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P6EPDB Entry 2P6E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629325.9% PEG1500, 0.2M NaCl, 0.1M NaCacodylate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1642.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.816α = 90
b = 91.549β = 111.9
c = 53.625γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.485098.70.10310.53.3692136830525.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.481.5393.70.77712.46433

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 REPLACEMENTTHROUGHOUTPDB Entry 2P6E1.4939.9264818345498.280.18870.18710.21958RANDOM28.389
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]
0.01-0.02-0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.678
r_dihedral_angle_4_deg16.125
r_dihedral_angle_3_deg13.926
r_dihedral_angle_1_deg6.361
r_scangle_it4.848
r_scbond_it3.295
r_mcangle_it2.294
r_angle_refined_deg2.216
r_mcbond_it1.46
r_chiral_restr0.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.678
r_dihedral_angle_4_deg16.125
r_dihedral_angle_3_deg13.926
r_dihedral_angle_1_deg6.361
r_scangle_it4.848
r_scbond_it3.295
r_mcangle_it2.294
r_angle_refined_deg2.216
r_mcbond_it1.46
r_chiral_restr0.247
r_bond_refined_d0.028
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3354
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms78

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling