X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch929315-20% PEG3400, 200 mM sodium chloride, 5 mM S-adenosylhomocysteine, 10 mM TDP-3-N,N-dimethylamino-3,6-dideoxyglucose, pH 9, batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.532α = 90
b = 92.05β = 106.1
c = 80.177γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.98789APS19-BM

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
11.65091.60.0690.06943.24.3123048123048
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)
11.61.6379.60.1760.1764.32.45330

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONPHASERTHROUGHOUTPDB ENTRY 3PFH1.641.24123048123048615091.420.182310.180560.21602RANDOM24.063
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]
0.14-2.21-0.020.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.448
r_dihedral_angle_4_deg20.249
r_dihedral_angle_3_deg13.57
r_dihedral_angle_1_deg6.823
r_angle_refined_deg2.025
r_angle_other_deg0.874
r_chiral_restr0.114
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.448
r_dihedral_angle_4_deg20.249
r_dihedral_angle_3_deg13.57
r_dihedral_angle_1_deg6.823
r_angle_refined_deg2.025
r_angle_other_deg0.874
r_chiral_restr0.114
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.001
r_bond_other_d
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7317
Nucleic Acid Atoms
Solvent Atoms647
Heterogen Atoms252

Software

Software
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling