5FKK

TetR(D) N82A mutant in complex with anhydrotetracycline and magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D7MPDB ENTRY 4D7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52951.5 M (NH4)2SO4, 0.1 M HEPES PH 7.5, 5% PEG 400, 0.2 M NACL, 1 MM 5A,6-ANHYDROTETRACYCLINE, 7.5 MM MGCL2 AT 295 K
Crystal Properties
Matthews coefficientSolvent content
2.2445.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.231α = 90
b = 68.231β = 90
c = 179.247γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX SX-165mmMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.7563.399.50.0830.98.543782-325.7
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)
11.751.7799.90.752.76.8

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 4D7M1.7563.2541206218398.670.208920.206520.25424RANDOM36.433
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]
0.830.83-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.852
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg12.747
r_dihedral_angle_1_deg5.144
r_mcangle_it2.315
r_scbond_it1.724
r_mcbond_other1.423
r_mcbond_it1.422
r_angle_refined_deg1.271
r_angle_other_deg0.747
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.852
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg12.747
r_dihedral_angle_1_deg5.144
r_mcangle_it2.315
r_scbond_it1.724
r_mcbond_other1.423
r_mcbond_it1.422
r_angle_refined_deg1.271
r_angle_other_deg0.747
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3162
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing