5DZ9

Streptococcus agalactiae AgI/II polypeptide BspA C-terminal domain (Mut)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WOY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M MMT buffer (1:2:2 L-Malic acid, MES, Tris-HCl pH 6.0) and 25% (w/v) PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.957.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.09α = 90
b = 48.24β = 90
c = 234.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9790DiamondI03

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
11.8958.5399.40.1117.212.335603
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)
11.891.940.8352482

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 REPLACEMENTTHROUGHOUT2WOY1.8958.5333734177899.320.196930.194680.24078RANDOM22.575
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]
-0.421.02-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.188
r_dihedral_angle_3_deg13.297
r_dihedral_angle_4_deg10.394
r_dihedral_angle_1_deg6.474
r_long_range_B_refined6.208
r_long_range_B_other6.015
r_scangle_other4.281
r_scbond_it2.799
r_scbond_other2.798
r_mcangle_it2.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.188
r_dihedral_angle_3_deg13.297
r_dihedral_angle_4_deg10.394
r_dihedral_angle_1_deg6.474
r_long_range_B_refined6.208
r_long_range_B_other6.015
r_scangle_other4.281
r_scbond_it2.799
r_scbond_other2.798
r_mcangle_it2.416
r_mcangle_other2.415
r_angle_refined_deg1.817
r_mcbond_it1.781
r_mcbond_other1.781
r_angle_other_deg0.869
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms2605
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
Cootmodel building
REFMACrefinement