7ZM4

Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclipostin-like inhibitor CyC31


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7ZJT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293MES Na 0.1 M NH4SO4 1.55 M PEG400 6.88%
Crystal Properties
Matthews coefficientSolvent content
2.6854.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.684α = 90
b = 87.224β = 90
c = 105.725γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978565SOLEILPROXIMA 1

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
11.6245.2199.70.0810.0840.0230.99917.213.59121119.648
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)
11.621.6494.71.4661.5280.4240.73812.3

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 REPLACEMENTTHROUGHOUT7ZJT1.6245.2186530464699.760.18460.18360.2022RANDOM24.242
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]
0.110.56-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.115
r_dihedral_angle_4_deg17.621
r_dihedral_angle_3_deg12.197
r_dihedral_angle_1_deg6.835
r_angle_refined_deg1.368
r_angle_other_deg1.356
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.115
r_dihedral_angle_4_deg17.621
r_dihedral_angle_3_deg12.197
r_dihedral_angle_1_deg6.835
r_angle_refined_deg1.368
r_angle_other_deg1.356
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4388
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms35

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing