2VQA

Protein-folding location can regulate Mn versus Cu- or Zn-binding. Crystal Structure of MncA.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.20.1M SODIUM ACETATE PH 3.25, 8% W/V PEG8000
Crystal Properties
Matthews coefficientSolvent content
4.270.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 236.19α = 90
b = 236.19β = 90
c = 134.041γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.9568.21000.1813.410.946724
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)
12.953.111000.435.611.2

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 1L3J2.9558.324429723861000.1930.1910.233RANDOM12.42
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]
-0.34-0.17-0.340.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.819
r_dihedral_angle_4_deg19.519
r_dihedral_angle_3_deg16.215
r_dihedral_angle_1_deg6.067
r_angle_refined_deg1.308
r_nbtor_refined0.331
r_symmetry_vdw_refined0.261
r_symmetry_hbond_refined0.253
r_nbd_refined0.232
r_xyhbond_nbd_refined0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.819
r_dihedral_angle_4_deg19.519
r_dihedral_angle_3_deg16.215
r_dihedral_angle_1_deg6.067
r_angle_refined_deg1.308
r_nbtor_refined0.331
r_symmetry_vdw_refined0.261
r_symmetry_hbond_refined0.253
r_nbd_refined0.232
r_xyhbond_nbd_refined0.155
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8236
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing