X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YC0pdb 1YC0, pdb 1FVD
experimental modelPDB 1FVDpdb 1YC0, pdb 1FVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.51:1 mixture of protein complex solution at 15 mg/mL and reservoir containing 20% PEG 10000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2645.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.82α = 98.39
b = 48.23β = 96.24
c = 97.05γ = 100.77
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.25094.40.04831.93251432514-234
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2874.50.21231.72563

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1YC0, pdb 1FVD2.247.51-23251430979153594.40.1950.195370.192780.24797RANDOM24.28
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]
0.18-0.01-0.1-0.62-0.440.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.927
r_dihedral_angle_4_deg16.975
r_dihedral_angle_3_deg13.984
r_dihedral_angle_1_deg5.88
r_scangle_it4.217
r_mcangle_it3.697
r_scbond_it2.864
r_mcbond_it2.369
r_angle_refined_deg1.164
r_symmetry_vdw_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.927
r_dihedral_angle_4_deg16.975
r_dihedral_angle_3_deg13.984
r_dihedral_angle_1_deg5.88
r_scangle_it4.217
r_mcangle_it3.697
r_scbond_it2.864
r_mcbond_it2.369
r_angle_refined_deg1.164
r_symmetry_vdw_refined0.222
r_nbd_refined0.204
r_symmetry_hbond_refined0.14
r_xyhbond_nbd_refined0.128
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5179
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing