5JF0 | pdb_00005jf0

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Arg


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52936% PEG-8000, 100mM Na Cacodylate pH6.5, 300mM Zn acetate
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.21α = 90
b = 65.43β = 90
c = 88.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.93950ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.65097.80.05920.076.023167622
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)
11.61.796.60.3285.46.14

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2AIE1.644.283005415821000.174160.172780.170.20020.2RANDOM17.54
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]
0.820.25-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.973
r_dihedral_angle_4_deg18.554
r_dihedral_angle_3_deg11.922
r_dihedral_angle_1_deg5.43
r_scangle_it3.384
r_scbond_it2.081
r_angle_refined_deg1.165
r_mcangle_it1.093
r_mcbond_it0.685
r_nbtor_refined0.303
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1603
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
FRODOmodel building
PHASERphasing