X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AFKOne molecule from PDB ID 1AFK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Phenylalanyl-O5'-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM in the soaking solution
Crystal Properties
Matthews coefficientSolvent content
2.1643.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.102α = 90
b = 32.5β = 90.42
c = 72.945γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Be (Beryllium lens)2019-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.4550980.0770.0830.0319.26.641463
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)
11.451.590.51.7181.9370.8690.3144.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTOne molecule from PDB ID 1AFK1.4530.9339307209397.790.19650.19460.2311RANDOM30.032
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]
-0.84-0.010.530.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.127
r_dihedral_angle_4_deg15.572
r_dihedral_angle_3_deg14.174
r_dihedral_angle_1_deg7.002
r_angle_refined_deg1.668
r_chiral_restr0.102
r_gen_planes_refined0.015
r_bond_refined_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1902
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing