X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.2 M Ammonium sulfate, 0.1 M BIS-TRIS, 25%(w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.149α = 90
b = 69.666β = 90
c = 123.476γ = 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
11.95099.30.06910.66.131133
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)
11.91.9798.10.6146.13022

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 REPLACEMENTTHROUGHOUT1YH31.95028138149994.530.1650.16250.2107RANDOM27.244
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]
0.260.96-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.986
r_sphericity_free24.384
r_dihedral_angle_4_deg15.977
r_dihedral_angle_3_deg13.588
r_dihedral_angle_1_deg6.047
r_sphericity_bonded4.15
r_angle_refined_deg1.303
r_rigid_bond_restr0.944
r_angle_other_deg0.906
r_mcangle_it0.883
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.986
r_sphericity_free24.384
r_dihedral_angle_4_deg15.977
r_dihedral_angle_3_deg13.588
r_dihedral_angle_1_deg6.047
r_sphericity_bonded4.15
r_angle_refined_deg1.303
r_rigid_bond_restr0.944
r_angle_other_deg0.906
r_mcangle_it0.883
r_mcbond_it0.728
r_mcbond_other0.722
r_chiral_restr0.076
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 Atoms2855
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms16

Software

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