5UMQ

Crystal structure of TnmS1, an antibiotic binding protein from Streptomyces sp. CB03234


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HC5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529850 mM ammonium sulphate, 50 mM bis-tris propane, and 30 % v/v pentaerythriol ethoxylate (15/4 EO/OH)
Crystal Properties
Matthews coefficientSolvent content
1.9436.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.569α = 90
b = 66.124β = 90
c = 103.354γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 315r2015-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.955098.40.0710.0740.020.9993313.118652
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9897.20.7610.8020.2420.882.49.6890

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 REPLACEMENTTHROUGHOUT4HC51.95501652389891.910.198430.195460.25621RANDOM23.311
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]
0.080.16-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.142
r_dihedral_angle_4_deg15.949
r_dihedral_angle_3_deg15.107
r_dihedral_angle_1_deg7.377
r_long_range_B_refined5.181
r_long_range_B_other5.085
r_mcangle_it2.765
r_mcangle_other2.765
r_scangle_other2.67
r_mcbond_it1.583
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.142
r_dihedral_angle_4_deg15.949
r_dihedral_angle_3_deg15.107
r_dihedral_angle_1_deg7.377
r_long_range_B_refined5.181
r_long_range_B_other5.085
r_mcangle_it2.765
r_mcangle_other2.765
r_scangle_other2.67
r_mcbond_it1.583
r_mcbond_other1.577
r_scbond_it1.559
r_scbond_other1.557
r_angle_refined_deg1.449
r_angle_other_deg0.951
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2000
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-3000data reduction
HKL-3000data scaling