7LU7

Human TDO (hTDO) in complex with NLG919 analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6PYZPDB entry 6PYZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH29350 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.263α = 90
b = 153.811β = 90
c = 87.975γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2017-01-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.29929.96899.70.9987.11.986779
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3498.90.9991.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 6PYZ2.329.9586779430499.6040.1920.18940.190.23640.2450.866
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]
-0.299-1.1151.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.561
r_dihedral_angle_3_deg17.514
r_dihedral_angle_4_deg17.34
r_lrange_other10.841
r_lrange_it10.837
r_scangle_it6.692
r_scangle_other6.692
r_mcangle_other6.229
r_mcangle_it6.228
r_dihedral_angle_1_deg5.41
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11364
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms320

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing