X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2M KSCN 25% PEG3350 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
238.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.687α = 90
b = 121.687β = 90
c = 39.955γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.631.831000.0550.05510.72.7197781977825.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.921000.4340.4341.72.62895

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT3DWY1.8231.83197741977410011000.16840.16840.16580.218RANDOM33.8217
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]
-1.62-0.81-1.622.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_dihedral_angle_4_deg15.1
r_dihedral_angle_3_deg14.33
r_scangle_it9.774
r_scbond_it7.49
r_dihedral_angle_1_deg6.049
r_mcangle_it4.75
r_mcbond_it3.515
r_angle_refined_deg1.509
r_mcbond_other1.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_dihedral_angle_4_deg15.1
r_dihedral_angle_3_deg14.33
r_scangle_it9.774
r_scbond_it7.49
r_dihedral_angle_1_deg6.049
r_mcangle_it4.75
r_mcbond_it3.515
r_angle_refined_deg1.509
r_mcbond_other1.159
r_angle_other_deg0.977
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1852
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms17

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction