3SGL

The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP73100.1M HEPES PH 7.0 30% (v/v) Jeffamine ED-2001 PH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 310K
Crystal Properties
Matthews coefficientSolvent content
2.5351.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.085α = 90
b = 59.815β = 100.18
c = 100.797γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9790NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.7501000.1430.1779.35.12157121571
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.751000.7340.8192.15.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3PVC2.75018983102292.680.184130.18010.25933RANDOM25.751
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]
-0.2-0.30.51-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.37
r_dihedral_angle_3_deg18.607
r_dihedral_angle_4_deg18.183
r_dihedral_angle_1_deg5.746
r_scangle_it4.774
r_scbond_it2.942
r_mcangle_it1.712
r_angle_refined_deg1.491
r_mcbond_it0.868
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.37
r_dihedral_angle_3_deg18.607
r_dihedral_angle_4_deg18.183
r_dihedral_angle_1_deg5.746
r_scangle_it4.774
r_scbond_it2.942
r_mcangle_it1.712
r_angle_refined_deg1.491
r_mcbond_it0.868
r_chiral_restr0.093
r_bond_refined_d0.013
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4916
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms81

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling