1JKR

Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IJW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM TRIS (PH 8.5), 10 MM CACL2, 23 MM NACL, 2.5% V/V PEG400, AND 1.56 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM TRIS (PH 8.5), 100 MM CACL2, 100 MM NACL, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%., pH 8.50, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.7653.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.087α = 90
b = 82.708β = 90
c = 44.865γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD1997-08-01MMOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL.
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
12.2824.893.230.8915.6817710269
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)
2.282.3872.140.2522.492.6

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENT1IJW2.2824.8710270793.230.26870.26870.3245RANDOM60.2
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]
15.1072.251-17.359
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.44
c_scangle_it15.66
c_scbond_it11.62
c_mcangle_it11.44
c_mcbond_it8.51
c_improper_angle_d1.882
c_angle_deg1.72
c_bond_d0.013
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.44
c_scangle_it15.66
c_scbond_it11.62
c_mcangle_it11.44
c_mcbond_it8.51
c_improper_angle_d1.882
c_angle_deg1.72
c_bond_d0.013
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 Atoms353
Nucleic Acid Atoms576
Solvent Atoms2
Heterogen Atoms8

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing