4MSO

X-ray crystal structure of a serine hydroxymethyl transferase in apo form from Burkholderia cenocepacia


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DFOPDB ENTRY 1DFO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289MCSG1 G8: 0.2 M ammonium sulfate, 0.1 M TRIS pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9938.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.28α = 90
b = 72.58β = 90
c = 182.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.45099.70.04723144864144410-320.058
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)
11.41.4499.70.5523.5

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 1DFO1.447.3144864144410724599.680.14760.14570.1824RANDOM19.1688
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]
0.06-0.150.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.039
r_sphericity_bonded14.545
r_dihedral_angle_4_deg14.354
r_dihedral_angle_3_deg11.569
r_dihedral_angle_1_deg7.389
r_rigid_bond_restr3.343
r_mcangle_it2.409
r_mcbond_other1.963
r_mcbond_it1.956
r_angle_refined_deg1.698
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.039
r_sphericity_bonded14.545
r_dihedral_angle_4_deg14.354
r_dihedral_angle_3_deg11.569
r_dihedral_angle_1_deg7.389
r_rigid_bond_restr3.343
r_mcangle_it2.409
r_mcbond_other1.963
r_mcbond_it1.956
r_angle_refined_deg1.698
r_angle_other_deg0.826
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5698
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms19

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction