5FKM

TetR(D) T103A mutant in complex with anhydrotetracycline and magnesium, I4(1)22


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52951.2 M (NH4)2SO4, 0.1 M MES PH 6.5, 110 MM NACL, 1 MM 5A,6-ANHYDROTETRACYCLINE, 7.5 MM MGCL2 AT 295 K
Crystal Properties
Matthews coefficientSolvent content
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.145α = 90
b = 68.145β = 90
c = 179.517γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDOSMIC MULTIPLE LAYER OPTICSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.6327.299.60.0821.910.726692-324.8
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)
11.631.7398.10.972.46.4

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 4D7M1.6327.1625356133599.610.171870.169820.21183RANDOM20.284
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]
0.340.34-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.381
r_dihedral_angle_4_deg16.151
r_dihedral_angle_3_deg12.721
r_dihedral_angle_1_deg5.127
r_angle_refined_deg1.645
r_mcangle_it1.462
r_scbond_it1.311
r_mcbond_it0.921
r_mcbond_other0.921
r_angle_other_deg0.851
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.381
r_dihedral_angle_4_deg16.151
r_dihedral_angle_3_deg12.721
r_dihedral_angle_1_deg5.127
r_angle_refined_deg1.645
r_mcangle_it1.462
r_scbond_it1.311
r_mcbond_it0.921
r_mcbond_other0.921
r_angle_other_deg0.851
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms1607
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing