7Q06

Crystal structure of TPADO in complex with 2-OH-TPA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N0Q3N0Q, 3EBY
experimental modelPDB 3EBY3N0Q, 3EBY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29312.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.8556.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 220.312α = 90
b = 220.312β = 90
c = 83.175γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.948190.79696.40.1090.0270.99917.917.3149913
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9482.05757.42.3720.560.591.418.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3N0Q, 3EBY1.95190.796149903722689.470.1670.16480.202243.123
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]
0.0270.0140.027-0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.374
r_dihedral_angle_4_deg17.993
r_dihedral_angle_3_deg14.079
r_dihedral_angle_1_deg7.482
r_lrange_it7.052
r_lrange_other7.046
r_scangle_other5.378
r_scangle_it5.377
r_mcangle_it3.94
r_mcangle_other3.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.374
r_dihedral_angle_4_deg17.993
r_dihedral_angle_3_deg14.079
r_dihedral_angle_1_deg7.482
r_lrange_it7.052
r_lrange_other7.046
r_scangle_other5.378
r_scangle_it5.377
r_mcangle_it3.94
r_mcangle_other3.94
r_scbond_it3.776
r_scbond_other3.772
r_mcbond_it2.835
r_mcbond_other2.835
r_angle_refined_deg1.814
r_angle_other_deg1.449
r_nbd_other0.243
r_symmetry_nbd_refined0.235
r_symmetry_xyhbond_nbd_other0.206
r_nbd_refined0.201
r_symmetry_nbd_other0.184
r_symmetry_xyhbond_nbd_refined0.171
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.152
r_ncsr_local_group_40.103
r_ncsr_local_group_20.1
r_ncsr_local_group_60.099
r_ncsr_local_group_10.098
r_ncsr_local_group_50.087
r_chiral_restr0.085
r_symmetry_nbtor_other0.082
r_ncsr_local_group_30.079
r_bond_refined_d0.014
r_xyhbond_nbd_other0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13861
Nucleic Acid Atoms
Solvent Atoms921
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing