3FOU

Low pH structure of the Rieske protein from Thermus thermophilus at 2.1 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NYKProtein A of 1NYK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.21298PEG 8000, Na Cacodylate, Calcium acetate, Pr(acetate)3, pH 6.21, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.152α = 90
b = 58.512β = 90
c = 58.798γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCMirrors2008-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.158.899.70.0884.523456
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)
12.0992.15499.80.5294.42311

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTProtein A of 1NYK2.158.82345622217120599.610.200720.200720.198060.24601RANDOM37.758
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]
0.43-0.480.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.266
r_dihedral_angle_3_deg16.693
r_dihedral_angle_4_deg14.699
r_dihedral_angle_1_deg6.876
r_scangle_it4.166
r_scbond_it2.623
r_angle_refined_deg1.862
r_mcangle_it1.759
r_mcbond_it1.079
r_metal_ion_refined0.436
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.266
r_dihedral_angle_3_deg16.693
r_dihedral_angle_4_deg14.699
r_dihedral_angle_1_deg6.876
r_scangle_it4.166
r_scbond_it2.623
r_angle_refined_deg1.862
r_mcangle_it1.759
r_mcbond_it1.079
r_metal_ion_refined0.436
r_symmetry_hbond_refined0.33
r_symmetry_vdw_refined0.324
r_nbtor_refined0.313
r_nbd_refined0.219
r_xyhbond_nbd_refined0.184
r_chiral_restr0.117
r_symmetry_metal_ion_refined0.072
r_bond_refined_d0.02
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2312
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms24

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling