4JCY

Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OR operator complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.0, 1 mM EDTA. Crystallisation conditions: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 6.0, 15 % (w/v) PEG3350, 10 mM spermidine, protein dimer/DNA molar ratio 1:1, protein concentration 4.6 mg/ml , VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4950.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.34α = 90
b = 62.34β = 90
c = 158.08γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELPSI PILATUS 6M2012-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.853.9999.50.05912.84.232091304762
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)
11.81.999.80.5512.64

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3LFP1.853.993209130476161499.90.147880.147120.1626RANDOM30.616
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]
0.410.41-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.751
r_dihedral_angle_4_deg12.664
r_dihedral_angle_3_deg11.329
r_dihedral_angle_1_deg4.041
r_angle_refined_deg0.952
r_chiral_restr0.066
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.751
r_dihedral_angle_4_deg12.664
r_dihedral_angle_3_deg11.329
r_dihedral_angle_1_deg4.041
r_angle_refined_deg0.952
r_chiral_restr0.066
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1494
Nucleic Acid Atoms855
Solvent Atoms402
Heterogen Atoms4

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling