1Y7O

The structure of Streptococcus pneumoniae A153P ClpP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293PEG 400, Calcium acetate, cacodylate, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.45149.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.65α = 90
b = 105.65β = 90
c = 236.192γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-11-05MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.9675,0.9950APS32-ID

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
12.529.50.05616.65.64750847508
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5971.10.2392.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD + MRTHROUGHOUTPDB ENTRY 1TYF2.5129.54750842825468088.990.192220.185980.24814RANDOM30.917
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]
0.830.410.83-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.533
r_scangle_it2.657
r_scbond_it1.574
r_angle_refined_deg1.302
r_mcangle_it1.132
r_angle_other_deg0.789
r_mcbond_it0.591
r_symmetry_hbond_refined0.288
r_nbd_other0.222
r_symmetry_vdw_other0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.533
r_scangle_it2.657
r_scbond_it1.574
r_angle_refined_deg1.302
r_mcangle_it1.132
r_angle_other_deg0.789
r_mcbond_it0.591
r_symmetry_hbond_refined0.288
r_nbd_other0.222
r_symmetry_vdw_other0.2
r_nbd_refined0.196
r_xyhbond_nbd_refined0.168
r_symmetry_vdw_refined0.143
r_metal_ion_refined0.121
r_nbtor_other0.086
r_chiral_restr0.072
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms9449
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing
CNXrefinement