1S99

The structure and function of B. subtilis YkoF gene product: ligand free protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529520% PEG 8000, 0.2 M calcium acetate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties
Matthews coefficientSolvent content
2.7655.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.93α = 90
b = 83.28β = 90
c = 85.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMARRESEARCHmirrors2003-08-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.9642, 0.9795, 0.9794APS22-ID

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
11.6340.24244.1212643512091-3
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)
1.61.6643.40.3221.92.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.6534.34779512651000.173530.172230.22375RANDOM23.29
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]
2.9-0.89-2.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.344
r_sphericity_free4.894
r_scangle_it4.166
r_scbond_it2.911
r_sphericity_bonded2.748
r_mcangle_it2.105
r_rigid_bond_restr1.691
r_angle_refined_deg1.517
r_mcbond_it1.337
r_angle_other_deg0.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.344
r_sphericity_free4.894
r_scangle_it4.166
r_scbond_it2.911
r_sphericity_bonded2.748
r_mcangle_it2.105
r_rigid_bond_restr1.691
r_angle_refined_deg1.517
r_mcbond_it1.337
r_angle_other_deg0.885
r_symmetry_vdw_other0.316
r_symmetry_hbond_refined0.282
r_nbd_other0.266
r_nbd_refined0.234
r_symmetry_vdw_refined0.209
r_xyhbond_nbd_refined0.169
r_chiral_restr0.098
r_nbtor_other0.088
r_metal_ion_refined0.068
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2819
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms9

Software

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