1KQ0

Human methionine aminopeptidase type II in complex with D-methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BN5PDB ENTRY 1BN5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527718-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.6741.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.727α = 90
b = 98.938β = 90
c = 100.628γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F2CHESSF2

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
125098.70.0776.7530241327.33
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)
22.1193.20.405142.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1BN525028701151698.70.192620.19130.21811RANDOM24.582
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]
-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it1.968
p_angle_d1.413
p_angle_deg1.413
p_scbond_it1.18
p_mcangle_it0.824
p_mcbond_it0.418
p_bond_d0.009
p_planar_d
p_hb_or_metal_coord
p_plane_restr
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it1.968
p_angle_d1.413
p_angle_deg1.413
p_scbond_it1.18
p_mcangle_it0.824
p_mcbond_it0.418
p_bond_d0.009
p_planar_d
p_hb_or_metal_coord
p_plane_restr
p_chiral_restr
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2782
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms11

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data scaling