2GS8

Structure of mevalonate pyrophosphate decarboxylase from Streptococcus pyogenes


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52910.1M sodium acetate trihydrate, 25% PEG 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9737.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.994α = 90
b = 72.065β = 90
c = 99.991γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-02-06MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97908, 0.97919APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.533.999.74351143511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5699.98.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.533.94351143511231699.70.166510.165090.19363RANDOM22.419
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]
-0.250.48-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.64
r_dihedral_angle_4_deg17.28
r_dihedral_angle_3_deg12.892
r_dihedral_angle_1_deg5.883
r_scangle_it4.184
r_scbond_it2.822
r_angle_refined_deg1.484
r_mcangle_it1.477
r_mcbond_it1.099
r_symmetry_vdw_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.64
r_dihedral_angle_4_deg17.28
r_dihedral_angle_3_deg12.892
r_dihedral_angle_1_deg5.883
r_scangle_it4.184
r_scbond_it2.822
r_angle_refined_deg1.484
r_mcangle_it1.477
r_mcbond_it1.099
r_symmetry_vdw_refined0.309
r_nbtor_refined0.306
r_symmetry_hbond_refined0.257
r_nbd_refined0.219
r_xyhbond_nbd_refined0.168
r_chiral_restr0.107
r_bond_refined_d0.013
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 Atoms2447
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
CCP4phasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
ARP/wARPmodel building
Cootmodel building