2HSG

Structure of transcription regulator CcpA in its DNA-free state


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82913% polyethylene glycol 8000, 100mM CaCl2, 10% (v/v) glycerol, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6152.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.464α = 90
b = 74.464β = 90
c = 238.923γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1997-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.95EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.53098.4143941415866.898
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)
2.52.56596.10.4363.7

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 REPLACEMENTTHROUGHOUTpdb entry 1SXH2.530134471415871198.260.2750.2810.2710.337RANDOM58.514
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]
1.360.681.36-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.646
r_dihedral_angle_4_deg21.272
r_dihedral_angle_3_deg18.675
r_dihedral_angle_1_deg8.653
r_mcangle_it2.191
r_angle_refined_deg1.616
r_scangle_it1.551
r_mcbond_it1.344
r_scbond_it0.998
r_angle_other_deg0.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.646
r_dihedral_angle_4_deg21.272
r_dihedral_angle_3_deg18.675
r_dihedral_angle_1_deg8.653
r_mcangle_it2.191
r_angle_refined_deg1.616
r_scangle_it1.551
r_mcbond_it1.344
r_scbond_it0.998
r_angle_other_deg0.809
r_symmetry_vdw_refined0.36
r_symmetry_vdw_other0.31
r_nbd_refined0.279
r_nbd_other0.237
r_xyhbond_nbd_refined0.228
r_symmetry_hbond_refined0.222
r_mcbond_other0.222
r_chiral_restr0.118
r_nbtor_other0.097
r_xyhbond_nbd_other0.086
r_gen_planes_refined0.015
r_bond_refined_d0.014
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2506
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing