X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.2M sodium acetate, 0.1M Tris-HCl, 25% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.448.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.141α = 90
b = 96.19β = 90
c = 143.254γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97852SSRFBL17U

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
12.25099.20.07413.47.624162
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)
12.22.281000.4617.62353

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 REPLACEMENTTHROUGHOUT1YH32.25022212120096.350.17130.16790.2366RANDOM34.51
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]
0.060.94-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.336
r_sphericity_free28.62
r_dihedral_angle_4_deg16.052
r_dihedral_angle_3_deg13.67
r_dihedral_angle_1_deg6.191
r_sphericity_bonded4.49
r_mcangle_it1.374
r_angle_refined_deg1.305
r_mcbond_it1.071
r_mcbond_other1.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.336
r_sphericity_free28.62
r_dihedral_angle_4_deg16.052
r_dihedral_angle_3_deg13.67
r_dihedral_angle_1_deg6.191
r_sphericity_bonded4.49
r_mcangle_it1.374
r_angle_refined_deg1.305
r_mcbond_it1.071
r_mcbond_other1.071
r_rigid_bond_restr0.951
r_angle_other_deg0.918
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2958
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection