1JKO

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 DROP7.5HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM HEPES (PH 7.5), 5 MM CACL2, 13 MM NACL, 2.8% V/V PEG400, AND 1.56 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM HEPES (PH 7.5), 50 MM CACL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%., pH 7.50, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6551.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.612α = 90
b = 81.996β = 90
c = 43.734γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate1997-09-01MMOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL.
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
12.241481.270.06819.715623567
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)
2.242.3450.80.2152.11.49

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 REPLACEMENT1IJW2.2414623563081.270.24390.24390.3057RANDOM64
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]
19.382.14-21.52
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.443
c_scangle_it9.24
c_mcangle_it6.22
c_scbond_it6.1
c_mcbond_it4.09
c_improper_angle_d1.489
c_angle_deg1.251
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.443
c_scangle_it9.24
c_mcangle_it6.22
c_scbond_it6.1
c_mcbond_it4.09
c_improper_angle_d1.489
c_angle_deg1.251
c_bond_d0.007
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 Atoms323
Nucleic Acid Atoms568
Solvent Atoms13
Heterogen Atoms8

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing