2HOF

Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6291MPD, SODIUM ACETATE, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.9558.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.625α = 90
b = 122.13β = 90
c = 178.748γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MONOCHROMATOR2003-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.078ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.45099.10.060.0513.74608245638
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4498.80.3970.3322255

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 REPLACEMENTTHROUGHOUT1CRX2.429.964608245516230998.770.240.240.2090.263RANDOM52.607
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]
0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.272
r_dihedral_angle_3_deg18.219
r_dihedral_angle_4_deg16.001
r_dihedral_angle_1_deg6.498
r_scangle_it2.413
r_angle_refined_deg1.452
r_scbond_it1.427
r_mcangle_it1.028
r_mcbond_it0.605
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.272
r_dihedral_angle_3_deg18.219
r_dihedral_angle_4_deg16.001
r_dihedral_angle_1_deg6.498
r_scangle_it2.413
r_angle_refined_deg1.452
r_scbond_it1.427
r_mcangle_it1.028
r_mcbond_it0.605
r_nbtor_refined0.293
r_symmetry_vdw_refined0.203
r_nbd_refined0.184
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.136
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4963
Nucleic Acid Atoms1394
Solvent Atoms501
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing