1SBR

The structure and function of B. subtilis YkoF gene product: the complex with thiamin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S99 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529520% PEG 8000, 0.2 M calcium acetate, 0.1 M MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.6753.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 82.49β = 90
c = 86.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IVMIRRORS2003-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS

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
12.3300.07518.44.716658-3
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)
2.32.3849.70.3062.83.2

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 REPLACEMENTTHROUGHOUT1S992.320157238361000.209150.206030.26881RANDOM55.8
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]
10.65-4.17-6.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.971
r_scangle_it3.861
r_scbond_it2.637
r_angle_refined_deg1.669
r_mcangle_it1.663
r_mcbond_it0.883
r_nbd_refined0.23
r_symmetry_vdw_refined0.2
r_chiral_restr0.186
r_xyhbond_nbd_refined0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.971
r_scangle_it3.861
r_scbond_it2.637
r_angle_refined_deg1.669
r_mcangle_it1.663
r_mcbond_it0.883
r_nbd_refined0.23
r_symmetry_vdw_refined0.2
r_chiral_restr0.186
r_xyhbond_nbd_refined0.152
r_metal_ion_refined0.141
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2788
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing