5B3A

Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52960.1 M HEPES sodium pH 7.5, 27% 2-propanol, 12% PEG4000, 12 mM TCEP-HCl, the crystal was soaked with the reservoir solution containing 5% MPD as a cryoprotectant, 20 mM O-phospho-L-serine (OPS) and 12 mM TCEP-HCl
Crystal Properties
Matthews coefficientSolvent content
2.2645.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.151α = 90
b = 74.151β = 90
c = 275.961γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDBruker DIP-60402009-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.1432.9297.9959.81040639
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.142.18

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTCysO free form (PDB ID, 3VSA)2.1432.9240639216197.990.144710.14170.20284RANDOM19.593
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.909
r_dihedral_angle_4_deg18.144
r_dihedral_angle_3_deg16.145
r_dihedral_angle_1_deg6.908
r_long_range_B_refined6.484
r_long_range_B_other6.404
r_scangle_other4.11
r_mcangle_other2.822
r_mcangle_it2.821
r_scbond_it2.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.909
r_dihedral_angle_4_deg18.144
r_dihedral_angle_3_deg16.145
r_dihedral_angle_1_deg6.908
r_long_range_B_refined6.484
r_long_range_B_other6.404
r_scangle_other4.11
r_mcangle_other2.822
r_mcangle_it2.821
r_scbond_it2.589
r_scbond_other2.589
r_angle_refined_deg1.941
r_mcbond_it1.812
r_mcbond_other1.809
r_angle_other_deg0.964
r_chiral_restr0.132
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5834
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling