1U05

Crystal structure of protein yfiH from Shigella flexneri, Pfam DUF152


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RW0PDB Entry 1RW0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Zinc Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.683α = 90.25
b = 50.465β = 96.51
c = 55.265γ = 90.29
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRANDEIS - B4mirrors2004-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C0.979NSLSX12C

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
12.5500.03513.22.2184771847725.8
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)
2.52.59950.0672.2

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 1RW02.5331847715869157697.90.2170.2170.283RANDOM21.9
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]
6.74-1.43-1.57-4.590.02-2.16
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.2
c_scangle_it2.53
c_angle_deg2
c_mcangle_it1.83
c_scbond_it1.8
c_improper_angle_d1.13
c_mcbond_it1.13
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.2
c_scangle_it2.53
c_angle_deg2
c_mcangle_it1.83
c_scbond_it1.8
c_improper_angle_d1.13
c_mcbond_it1.13
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3710
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms2

Software

Software
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data scaling
AMoREphasing