2OOG

Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5294O.1M HEPES PH 7.5, 25% PEG 3350, 0.2M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.1961.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.312α = 90
b = 183.546β = 90
c = 176.79γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2006-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97940APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.25097.10.0580.05485.712406512406547.63
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2897.10.320.361.84.512275

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YDY2.220120201120201374297.160.23620.234840.28044RANDOM56.26
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]
-1.891.050.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.272
r_dihedral_angle_3_deg18.704
r_dihedral_angle_4_deg16.105
r_scangle_it14.218
r_scbond_it11.081
r_dihedral_angle_1_deg10.814
r_mcangle_it9.072
r_mcbond_it7.139
r_angle_refined_deg1.133
r_nbtor_refined0.292
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.272
r_dihedral_angle_3_deg18.704
r_dihedral_angle_4_deg16.105
r_scangle_it14.218
r_scbond_it11.081
r_dihedral_angle_1_deg10.814
r_mcangle_it9.072
r_mcbond_it7.139
r_angle_refined_deg1.133
r_nbtor_refined0.292
r_symmetry_hbond_refined0.217
r_xyhbond_nbd_refined0.172
r_chiral_restr0.162
r_nbd_refined0.137
r_symmetry_vdw_refined0.132
r_metal_ion_refined0.014
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_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 Atoms13120
Nucleic Acid Atoms
Solvent Atoms891
Heterogen Atoms270

Software

Software
Software NamePurpose
PHASERphasing
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling