X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W9I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529850mM Na Acetate-HCl pH5.0, 300mM NaCl, 25% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.4864.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.949α = 87.53
b = 134.343β = 70.2
c = 149.692γ = 89.02
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.9140.7398.90.0570.0660.03312.63.9199569
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.9598.70.7530.8730.4410.7863.9

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 REPLACEMENTTHROUGHOUT3W9I2.91140.73174254919692.710.23610.23390.2777RANDOM54.214
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]
-0.451.18-0.48-0.220.440.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.629
r_dihedral_angle_4_deg18.27
r_dihedral_angle_3_deg17.743
r_dihedral_angle_1_deg6.088
r_angle_refined_deg1.662
r_angle_other_deg1.098
r_chiral_restr0.089
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.629
r_dihedral_angle_4_deg18.27
r_dihedral_angle_3_deg17.743
r_dihedral_angle_1_deg6.088
r_angle_refined_deg1.662
r_angle_other_deg1.098
r_chiral_restr0.089
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms46738
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms138

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing