3AD7

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X31PDB ENTRY 1X31

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1M TRIS-HCL, 1.9M AMMONIUM SULFATE, 10MM CUSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1560.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 198.949α = 90
b = 198.949β = 90
c = 196.765γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102005-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0000SPring-8BL26B1

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
12.239.621000.0830.08318.88.611587030.1
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)
12.22.321000.2258.7146098

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1X312.239.5310999458041000.171550.169780.20455RANDOM27.183
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]
0.030.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.914
r_dihedral_angle_4_deg16.771
r_dihedral_angle_3_deg14.335
r_dihedral_angle_1_deg6.645
r_scangle_it3.914
r_scbond_it2.631
r_angle_refined_deg1.605
r_mcangle_it1.502
r_mcbond_it0.947
r_symmetry_vdw_refined0.411
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.914
r_dihedral_angle_4_deg16.771
r_dihedral_angle_3_deg14.335
r_dihedral_angle_1_deg6.645
r_scangle_it3.914
r_scbond_it2.631
r_angle_refined_deg1.605
r_mcangle_it1.502
r_mcbond_it0.947
r_symmetry_vdw_refined0.411
r_nbtor_refined0.307
r_nbd_refined0.208
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.116
r_chiral_restr0.113
r_bond_refined_d0.018
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 Atoms12519
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms180

Software

Software
Software NamePurpose
SPACEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling