3PX2

Structure of TylM1 from Streptomyces fradiae H123N mutant in complex with SAH and dTDP-Quip3N


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PFHPDB entry 3PFH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529516% PEG 5000 monomethyl-ether, 2% 1,4-dioxane, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.571α = 90
b = 40.703β = 117.93
c = 87.208γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montell2010-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.6577.193.40.0810.0819.63.46095860958
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.7583.40.390.391.81.58728

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3PFH1.6577.056094860948307393.450.196690.196690.194170.24458RANDOM16.534
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]
-0.160.060.34-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.379
r_dihedral_angle_4_deg22.201
r_dihedral_angle_3_deg15.814
r_dihedral_angle_1_deg7.104
r_scangle_it5.7
r_scbond_it4.033
r_mcangle_it2.554
r_angle_refined_deg2.286
r_mcbond_it1.759
r_chiral_restr0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.379
r_dihedral_angle_4_deg22.201
r_dihedral_angle_3_deg15.814
r_dihedral_angle_1_deg7.104
r_scangle_it5.7
r_scbond_it4.033
r_mcangle_it2.554
r_angle_refined_deg2.286
r_mcbond_it1.759
r_chiral_restr0.214
r_bond_refined_d0.014
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3658
Nucleic Acid Atoms
Solvent Atoms414
Heterogen Atoms130

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling