5GO5

Structure of sortase E from Streptomyces avermitilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RCC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.752931.6M ammonium sulfate, 0.1M citric acid pH 3.75
Crystal Properties
Matthews coefficientSolvent content
2.346.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.84α = 90
b = 85.84β = 90
c = 48.2γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2014-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.6542.9299.90.0750.99919.39.32490326.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.20.7780.8083.39.4

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 REPLACEMENTFREE R-VALUE3RCC1.6542.9223644124399.790.162720.161240.19078RANDOM20.39
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]
0.180.090.18-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.896
r_dihedral_angle_4_deg13.685
r_dihedral_angle_3_deg9.94
r_dihedral_angle_1_deg6.237
r_long_range_B_refined6.196
r_long_range_B_other5.843
r_scangle_other3.717
r_mcangle_it2.435
r_mcangle_other2.435
r_scbond_it2.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.896
r_dihedral_angle_4_deg13.685
r_dihedral_angle_3_deg9.94
r_dihedral_angle_1_deg6.237
r_long_range_B_refined6.196
r_long_range_B_other5.843
r_scangle_other3.717
r_mcangle_it2.435
r_mcangle_other2.435
r_scbond_it2.412
r_scbond_other2.396
r_mcbond_it1.616
r_mcbond_other1.583
r_angle_refined_deg1.58
r_angle_other_deg0.985
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms1197
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing