6RBM

TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FPL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295precipitant: 0.5M (NH4)2SO4, 0.68M Li2SO4, 0.1M Na-citrate, protein: 0.1mL protein, 0.1mL 2mM minoTc, 0.0005mL 3M MgCl2, 100 mM NaCl, 50 mM Tris pH 8.0, ratio 2/2
Crystal Properties
Matthews coefficientSolvent content
2.244.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.67α = 90
b = 67.67β = 90
c = 178.74γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252011-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.95000BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.0563.399.10.05322.747.11339743.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1799.51.092.467.15

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 REPLACEMENTTHROUGHOUT6FPL2.0547.912379102899.240.215530.211340.26329RANDOM53.247
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]
1.271.27-2.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.567
r_dihedral_angle_3_deg17.187
r_dihedral_angle_4_deg16.55
r_dihedral_angle_1_deg7.337
r_long_range_B_refined6.912
r_long_range_B_other6.911
r_scangle_other4.453
r_mcangle_it4.414
r_mcangle_other4.412
r_mcbond_it2.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.567
r_dihedral_angle_3_deg17.187
r_dihedral_angle_4_deg16.55
r_dihedral_angle_1_deg7.337
r_long_range_B_refined6.912
r_long_range_B_other6.911
r_scangle_other4.453
r_mcangle_it4.414
r_mcangle_other4.412
r_mcbond_it2.872
r_mcbond_other2.872
r_scbond_it2.87
r_scbond_other2.869
r_angle_refined_deg1.84
r_angle_other_deg1.382
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1619
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing