X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YH3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.1M Tris, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.0559.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.552α = 90
b = 96.242β = 90
c = 133.777γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9793SSRFBL17U

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
12.35099.70.0929.79.851358
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)
12.32.381000.5769.15075

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 REPLACEMENTTHROUGHOUT1YH32.35042953225987.750.19960.1980.2313RANDOM42.654
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]
-2.590.372.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.191
r_sphericity_free30.549
r_dihedral_angle_4_deg20.424
r_dihedral_angle_3_deg14.514
r_dihedral_angle_1_deg5.765
r_sphericity_bonded3.163
r_rigid_bond_restr1.459
r_angle_refined_deg1.383
r_angle_other_deg1.181
r_mcangle_it0.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.191
r_sphericity_free30.549
r_dihedral_angle_4_deg20.424
r_dihedral_angle_3_deg14.514
r_dihedral_angle_1_deg5.765
r_sphericity_bonded3.163
r_rigid_bond_restr1.459
r_angle_refined_deg1.383
r_angle_other_deg1.181
r_mcangle_it0.658
r_mcbond_it0.507
r_mcbond_other0.507
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5755
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data processing