2JCG

Apo form of the catabolite control protein A (ccpA) from bacillus megaterium, with the DNA binding domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
183% PEG 3000, 100 MM CACL2, 10% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.45α = 90
b = 74.45β = 90
c = 238.84γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.63098.60.0524.86.514161-3
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)
12.62.70.443.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1SXG2.619.611615103698.70.2340.2290.297RANDOM46.14
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]
0.090.050.09-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.023
r_dihedral_angle_4_deg20.22
r_dihedral_angle_3_deg17.519
r_dihedral_angle_1_deg5.984
r_scangle_it4.118
r_scbond_it2.568
r_angle_refined_deg1.3
r_mcangle_it0.862
r_mcbond_it0.437
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.023
r_dihedral_angle_4_deg20.22
r_dihedral_angle_3_deg17.519
r_dihedral_angle_1_deg5.984
r_scangle_it4.118
r_scbond_it2.568
r_angle_refined_deg1.3
r_mcangle_it0.862
r_mcbond_it0.437
r_nbtor_refined0.308
r_nbd_refined0.218
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.142
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2427
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing