5ZH8

Crystal Structure of FmtA from Staphylococcus aureus at 2.58 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9737.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.391α = 90
b = 128.234β = 90
c = 107.599γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.585095.70.9813.283.42278455.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.582.62280.582.12

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 REPLACEMENTTHROUGHOUT4GDN2.65021118111897.560.209930.207650.25436RANDOM72.845
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]
0.36-0.790.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.798
r_dihedral_angle_3_deg14.535
r_dihedral_angle_4_deg13.868
r_dihedral_angle_1_deg5.62
r_long_range_B_refined2.13
r_long_range_B_other2.06
r_angle_refined_deg1.032
r_angle_other_deg0.714
r_mcangle_it0.646
r_mcangle_other0.646
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.798
r_dihedral_angle_3_deg14.535
r_dihedral_angle_4_deg13.868
r_dihedral_angle_1_deg5.62
r_long_range_B_refined2.13
r_long_range_B_other2.06
r_angle_refined_deg1.032
r_angle_other_deg0.714
r_mcangle_it0.646
r_mcangle_other0.646
r_scangle_other0.401
r_mcbond_it0.35
r_mcbond_other0.35
r_scbond_it0.208
r_scbond_other0.207
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5779
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
Cootmodel building