7F5N

Crystal structure of TCPTP catalytic domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52910.15 M Ammonium nitrate, 0.1 M MES (pH-6.0), 20% v/v PEG smear medium, 5% v/v Ethylene glycol and 5.5 mM lysine dipeptide additive
Crystal Properties
Matthews coefficientSolvent content
2.1442.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.57α = 112.932
b = 68.056β = 106.459
c = 73.244γ = 92.459
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107CCDRAYONIX MX300HE2019-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9320920.0170.9941.62.263299
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.93296.30.0830.989.72.2

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-VALUE1L8K1.9319.94862827312091.1780.1860.18340.237624.787
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]
-0.1530.090.072-0.0640.0170.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg21.1
r_dihedral_angle_3_deg18.566
r_dihedral_angle_1_deg6.903
r_lrange_it6.024
r_lrange_other5.966
r_scangle_it4.225
r_scangle_other4.224
r_mcangle_it3.296
r_mcangle_other3.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg21.1
r_dihedral_angle_3_deg18.566
r_dihedral_angle_1_deg6.903
r_lrange_it6.024
r_lrange_other5.966
r_scangle_it4.225
r_scangle_other4.224
r_mcangle_it3.296
r_mcangle_other3.296
r_scbond_it2.649
r_scbond_other2.648
r_mcbond_it2.202
r_mcbond_other2.2
r_angle_refined_deg1.616
r_angle_other_deg1.353
r_nbd_other0.276
r_symmetry_nbd_refined0.247
r_nbd_refined0.207
r_symmetry_xyhbond_nbd_refined0.19
r_symmetry_nbd_other0.188
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.167
r_symmetry_nbtor_other0.088
r_chiral_restr0.085
r_symmetry_xyhbond_nbd_other0.045
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7191
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms

Software

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