X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSyrB2 with Fe(II), chloride, and alpha-ketoglutarate

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277.1515% PEG 3350, 250 mM Na formate, spermine tetra-HCl, n-decanoyl sucrose , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.12α = 90
b = 89.35β = 90
c = 125.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHdouble crystal monochromator2005-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9195SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.842.1895.30.07218.27.6572155721517.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.986.40.3372.45.97474

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODYTHROUGHOUTSyrB2 with Fe(II), chloride, and alpha-ketoglutarate1.842.185649856498334193.980.1730.1730.1710.21Same as starting model17.096
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]
-0.23-0.110.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.644
r_dihedral_angle_3_deg14.486
r_dihedral_angle_4_deg13.923
r_dihedral_angle_1_deg6.836
r_scangle_it3.437
r_scbond_it2.474
r_mcangle_it1.535
r_angle_refined_deg1.532
r_mcbond_it1.387
r_angle_other_deg1.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.644
r_dihedral_angle_3_deg14.486
r_dihedral_angle_4_deg13.923
r_dihedral_angle_1_deg6.836
r_scangle_it3.437
r_scbond_it2.474
r_mcangle_it1.535
r_angle_refined_deg1.532
r_mcbond_it1.387
r_angle_other_deg1.345
r_symmetry_vdw_other0.282
r_mcbond_other0.252
r_nbd_refined0.208
r_nbd_other0.203
r_nbtor_refined0.187
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.152
r_chiral_restr0.097
r_nbtor_other0.089
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4814
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms60

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
CNSphasing