1XAF | pdb_00001xaf

Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295PEG 3350, Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.246

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.874α = 90.32
b = 50.583β = 96.32
c = 55.347γ = 90.4
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-2mirrors2004-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-ID

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
12.0155.0597.40.07111.34.73135530856
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)
12.012.0889.60.2066.53.92849

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.0155.052758227582307196.910.185830.185830.17860.1780.251590.2514RANDOM22.5
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]
0.98-0.07-0.81-0.790.03-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.409
r_dihedral_angle_4_deg19.485
r_dihedral_angle_3_deg16.65
r_dihedral_angle_1_deg6.668
r_scangle_it3.619
r_scbond_it2.617
r_angle_refined_deg1.517
r_mcangle_it1.505
r_mcbond_it1.061
r_symmetry_vdw_refined0.302
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3688
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing