2FU2

Crystal structure of protein SPy2152 from Streptococcus pyogenes


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629020 % PEG 8000, Mes pH 6.0, Ca(OAc)2 , VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.6525.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.087α = 90
b = 30.28β = 113.26
c = 35.855γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97907APS19-ID

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
12.015091.10.08730.266.651394682-3
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)
12.012.0358.60.2833.624.175

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.1534.943855385518596.050.16110.161110.157320.25389RANDOM35.876
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]
3.81-0.16-2.12-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.803
r_dihedral_angle_3_deg16.81
r_dihedral_angle_4_deg14.406
r_dihedral_angle_1_deg6.349
r_scangle_it4.323
r_scbond_it2.888
r_angle_refined_deg1.813
r_mcangle_it1.538
r_mcbond_it0.95
r_symmetry_vdw_refined0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.803
r_dihedral_angle_3_deg16.81
r_dihedral_angle_4_deg14.406
r_dihedral_angle_1_deg6.349
r_scangle_it4.323
r_scbond_it2.888
r_angle_refined_deg1.813
r_mcangle_it1.538
r_mcbond_it0.95
r_symmetry_vdw_refined0.33
r_nbtor_refined0.319
r_symmetry_hbond_refined0.272
r_nbd_refined0.235
r_xyhbond_nbd_refined0.221
r_chiral_restr0.102
r_bond_refined_d0.026
r_gen_planes_refined0.007
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms627
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building