3NWO

Crystal structure of Proline iminopeptidase Mycobacterium smegmatis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320% PEG 3350, 0.2 M sodium citrate, 0.1 M Tris propane, pH 8.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.93α = 90
b = 69.92β = 93.18
c = 55.63γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-05-14SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.85094.80.11712.8724228-317.989
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)
11.81.8555.80.5272.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.937.9421658110499.490.1380.1360.173RANDOM10.295
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]
0.230.17-0.17-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.803
r_dihedral_angle_4_deg20.089
r_dihedral_angle_3_deg12.861
r_dihedral_angle_1_deg5.757
r_scangle_it2.93
r_scbond_it1.904
r_angle_refined_deg1.412
r_mcangle_it1.112
r_angle_other_deg0.957
r_mcbond_it0.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.803
r_dihedral_angle_4_deg20.089
r_dihedral_angle_3_deg12.861
r_dihedral_angle_1_deg5.757
r_scangle_it2.93
r_scbond_it1.904
r_angle_refined_deg1.412
r_mcangle_it1.112
r_angle_other_deg0.957
r_mcbond_it0.668
r_mcbond_other0.208
r_chiral_restr0.089
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2304
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms17

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction