4CKK | pdb_00004ckk

Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y3PPDB ENTRY 2Y3P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.9659

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.57α = 105.16
b = 95.53β = 118.81
c = 95.89γ = 103.42
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
11.981.51970.07112.919450923.6
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)
11.91.9594.70.492.72.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Y3P1.981.51184697979996.970.170310.169350.180.188590.19RANDOM32.3
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]
0.130.060.590.220.40.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.591
r_dihedral_angle_4_deg16.352
r_dihedral_angle_3_deg12.418
r_dihedral_angle_1_deg5.218
r_scbond_it2.244
r_mcangle_it1.871
r_angle_refined_deg1.502
r_angle_other_deg1.312
r_mcbond_it1.228
r_mcbond_other1.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.591
r_dihedral_angle_4_deg16.352
r_dihedral_angle_3_deg12.418
r_dihedral_angle_1_deg5.218
r_scbond_it2.244
r_mcangle_it1.871
r_angle_refined_deg1.502
r_angle_other_deg1.312
r_mcbond_it1.228
r_mcbond_other1.228
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.007
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms15016
Nucleic Acid Atoms
Solvent Atoms1056
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing