9EMW | pdb_00009emw

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 Y7F Mutant bound to ImmH-Forodesine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F62 
experimental modelPDB 3EHD 
experimental modelPDB 6EVS 
experimental modelPDB 6QAI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.1 M Tris pH 8.0, 0.002 M Zinc chloride, 20% w/v PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.3162.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.76α = 90
b = 135.76β = 90
c = 87.55γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS EIGER2 XE 16M2022-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.4470.2199.120.160.1650.0380.9979.416.133966
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)
12.442.481.8332.0360.8590.2950.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5170.2129897156599.820.190260.187180.20450.252610.27RANDOM71.296
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]
1.190.591.19-3.85
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other20.054
r_long_range_B_refined20.053
r_scangle_other16.347
r_dihedral_angle_3_deg16.053
r_dihedral_angle_2_deg12.929
r_scbond_it12.066
r_scbond_other12.064
r_mcangle_it10.984
r_mcangle_other10.982
r_mcbond_it8.256
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other20.054
r_long_range_B_refined20.053
r_scangle_other16.347
r_dihedral_angle_3_deg16.053
r_dihedral_angle_2_deg12.929
r_scbond_it12.066
r_scbond_other12.064
r_mcangle_it10.984
r_mcangle_other10.982
r_mcbond_it8.256
r_mcbond_other8.25
r_dihedral_angle_1_deg7.553
r_angle_refined_deg2.385
r_angle_other_deg0.903
r_chiral_restr0.114
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.003
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5033
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHENIXphasing