5ZHI

Apo crystal structure of TrmD from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelITasserhomology modeling from I-TASSER server

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293100mM Bis-Tris at pH 6.5, 20%(w/v) PEG3350, 0.1M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
1.9737.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.17α = 90
b = 113.07β = 110.75
c = 44.21γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
12.241.396.10.05516.13.719717
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)
12.22.2791.80.2263.5

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 REPLACEMENTTHROUGHOUThomology modeling from I-TASSER server2.238.831870898395.540.161590.159580.170.20010.2RANDOM19.463
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]
-7.73-3.0313.05-5.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.249
r_dihedral_angle_4_deg22.544
r_dihedral_angle_3_deg16.303
r_dihedral_angle_1_deg6.376
r_long_range_B_refined5.718
r_long_range_B_other5.707
r_scangle_other3.157
r_mcangle_it2.929
r_mcangle_other2.928
r_scbond_it2.017
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3245
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing