4PNC

E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH INHIBITOR 7-METHOXY-2-METHYLEN-3,4-DIHYDRONAPHTHALEN-1(2H)-ONE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.1293PEG 4000, COBALT CHLORIDE, HEPES, METHIONINE, SODIUM CHLORIDE, POTASSIUM CHLORIDE, PH 7.1
Crystal Properties
Matthews coefficientSolvent content
1.9938.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.01α = 90
b = 66.82β = 111.15
c = 48.45γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMONTEL MIRRORS2008-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.5418

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
11.543092.10.02531.093.26107317.883
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)
11.551.684.60.11310.673.01

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.5419.6929747156691.970.133730.132050.16533RANDOM12.864
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]
-0.08-0.410.78-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg18.428
r_dihedral_angle_3_deg11.565
r_long_range_B_refined6.782
r_dihedral_angle_1_deg6.397
r_long_range_B_other6.34
r_scangle_other3.81
r_scbond_it2.511
r_scbond_other2.51
r_angle_refined_deg2.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg18.428
r_dihedral_angle_3_deg11.565
r_long_range_B_refined6.782
r_dihedral_angle_1_deg6.397
r_long_range_B_other6.34
r_scangle_other3.81
r_scbond_it2.511
r_scbond_other2.51
r_angle_refined_deg2.272
r_mcangle_other1.983
r_mcangle_it1.955
r_mcbond_it1.3
r_mcbond_other1.21
r_angle_other_deg0.963
r_chiral_restr0.129
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2032
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata scaling
XSCALEdata scaling
Cootmodel building
HKL2Mapmodel building
SHELXCDphasing
ARP/wARPmodel building