X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VYN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529120% PEG5000MME, 0.2mM Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.9157.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.644α = 89.04
b = 75.534β = 89.96
c = 94.143γ = 92.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2015-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
11.75097.30.0680.0780.0417.63.7153919
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7395.70.80.5440.5773.58817

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 REPLACEMENTTHROUGHOUT3VYN1.7950144115737194.720.17160.16960.21RANDOM17.48
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]
0.170.040.1-0.25-0.070.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.349
r_dihedral_angle_4_deg18.412
r_dihedral_angle_3_deg12.948
r_dihedral_angle_1_deg6.364
r_mcangle_it2.398
r_angle_refined_deg1.991
r_mcbond_it1.566
r_mcbond_other1.566
r_angle_other_deg1.103
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.349
r_dihedral_angle_4_deg18.412
r_dihedral_angle_3_deg12.948
r_dihedral_angle_1_deg6.364
r_mcangle_it2.398
r_angle_refined_deg1.991
r_mcbond_it1.566
r_mcbond_other1.566
r_angle_other_deg1.103
r_chiral_restr0.154
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10558
Nucleic Acid Atoms
Solvent Atoms1827
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction