5AGE | pdb_00005age

CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A BENZOMORPHOLINONE LIGAND


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H5ZPDB ENTRY 3H5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.525.9%PEG1500,0.2M NACL, 0.1M CACODYLATE, PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.2144.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.024α = 90
b = 90.165β = 113.78
c = 52.966γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE2011-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
122092.30.06222.12580028
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0385.60.362.71.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3H5Z219.7524432131992.040.176930.173680.180.235160.23RANDOM30.722
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]
0.120.04-0.07-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.622
r_dihedral_angle_4_deg19.772
r_dihedral_angle_3_deg16.039
r_dihedral_angle_1_deg6.932
r_scangle_it4.552
r_scbond_it3.075
r_angle_refined_deg1.976
r_mcangle_it1.952
r_mcbond_it1.155
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.622
r_dihedral_angle_4_deg19.772
r_dihedral_angle_3_deg16.039
r_dihedral_angle_1_deg6.932
r_scangle_it4.552
r_scbond_it3.075
r_angle_refined_deg1.976
r_mcangle_it1.952
r_mcbond_it1.155
r_chiral_restr0.15
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3344
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing