8R1M | pdb_00008r1m

Structure of TxGH116 with covalently bound N-azido-octyl aziridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BVU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6291PEG 3000, ammonium sulfate, MES buffer
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.975α = 90
b = 165.149β = 90
c = 178.921γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95374DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.956.161000.0790.9967.110.7129333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.6430.5541.310.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.956.095129077630099.8630.1790.17710.17710.22650.2265RANDOM24.829
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]
1.7060.26-1.966
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.434
r_dihedral_angle_3_deg13.443
r_dihedral_angle_1_deg7.129
r_dihedral_angle_2_deg6.114
r_lrange_it4.575
r_lrange_other4.575
r_scangle_it3.25
r_scangle_other3.249
r_mcangle_it2.799
r_mcangle_other2.799
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.434
r_dihedral_angle_3_deg13.443
r_dihedral_angle_1_deg7.129
r_dihedral_angle_2_deg6.114
r_lrange_it4.575
r_lrange_other4.575
r_scangle_it3.25
r_scangle_other3.249
r_mcangle_it2.799
r_mcangle_other2.799
r_scbond_it2.092
r_scbond_other2.092
r_mcbond_it1.867
r_mcbond_other1.867
r_angle_refined_deg1.512
r_angle_other_deg0.593
r_metal_ion_refined0.241
r_nbd_refined0.214
r_symmetry_nbd_other0.203
r_nbtor_refined0.19
r_symmetry_xyhbond_nbd_refined0.171
r_xyhbond_nbd_refined0.167
r_nbd_other0.153
r_symmetry_nbd_refined0.126
r_ncsr_local_group_10.1
r_symmetry_nbtor_other0.084
r_chiral_restr0.077
r_symmetry_xyhbond_nbd_other0.043
r_gen_planes_other0.014
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12403
Nucleic Acid Atoms
Solvent Atoms880
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing