3JRB

Crystal structure of Fis bound to 27 bp DNA F24 containing T-tract at center


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IV5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.2 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 36% PEG 400, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.0869.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.573α = 90
b = 94.264β = 90
c = 155.336γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.000ALS8.2.2

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
13.19099.20.1416.74.611692
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)
13.13.21990.6264.61130

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 REPLACEMENTTHROUGHOUT3IV53.180.581165955795.070.2420.2390.29RANDOM75.589
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.756
r_dihedral_angle_3_deg19.999
r_dihedral_angle_4_deg12.462
r_dihedral_angle_1_deg6.848
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)3.8
MAIN-CHAIN BOND REFINED ATOMS (A''2)2.961
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)2.435
r_angle_refined_deg1.739
SIDE-CHAIN BOND REFINED ATOMS (A''2)1.532
r_angle_other_deg1.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.756
r_dihedral_angle_3_deg19.999
r_dihedral_angle_4_deg12.462
r_dihedral_angle_1_deg6.848
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)3.8
MAIN-CHAIN BOND REFINED ATOMS (A''2)2.961
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)2.435
r_angle_refined_deg1.739
SIDE-CHAIN BOND REFINED ATOMS (A''2)1.532
r_angle_other_deg1.109
r_symmetry_hbond_refined0.449
MAIN-CHAIN BOND OTHER ATOMS (A''2)0.444
r_nbd_refined0.234
r_nbtor_refined0.215
r_nbd_other0.207
r_symmetry_vdw_other0.207
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.159
r_nbtor_other0.088
CHIRAL-CENTER RESTRAINTS (A''3)0.07
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1505
Nucleic Acid Atoms1101
Solvent Atoms15
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing