3FMR

Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor TNP470 bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FM3PDB entry 3FM3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29327% PEG 4000, 0.2M Ammonium sulfate, 0.5mM TNP470. Cryosolution: 30% PEG 4000, 0.2M Ammonium sulfate, 10% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.977α = 90
b = 94.067β = 99.33
c = 66.407γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
12.895099.20.1737.4745.316725
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)
12.89398.80.4735.31640

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3FM32.89501671084298.860.1830.1780.266RANDOM25.604
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]
0.230.01-0.480.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.237
r_dihedral_angle_4_deg22.615
r_dihedral_angle_3_deg17.327
r_dihedral_angle_1_deg5.834
r_scangle_it2.084
r_angle_refined_deg1.209
r_scbond_it1.199
r_mcangle_it0.791
r_mcbond_it0.401
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.237
r_dihedral_angle_4_deg22.615
r_dihedral_angle_3_deg17.327
r_dihedral_angle_1_deg5.834
r_scangle_it2.084
r_angle_refined_deg1.209
r_scbond_it1.199
r_mcangle_it0.791
r_mcbond_it0.401
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5506
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms72

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing