X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMODEL IN DIFFERENT SPACE GROUP OBTAINED FROM IODIDE PHASING

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2846.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.45α = 90
b = 88.45β = 90
c = 142.68γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

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
11.55099.50.04416.383.6100819100352-323.829
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)
11.51.5499.20.392.43

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 REPLACEMENTTHROUGHOUTMODEL IN DIFFERENT SPACE GROUP OBTAINED FROM IODIDE PHASING1.550100819100315484899.540.15590.15590.15460.1826RANDOM19.044
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]
-0.4-0.2-0.41.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.101
r_dihedral_angle_4_deg19.553
r_dihedral_angle_3_deg12.072
r_dihedral_angle_1_deg5.755
r_angle_refined_deg1.556
r_mcangle_it1.409
r_mcbond_it0.869
r_angle_other_deg0.859
r_mcbond_other0.856
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.101
r_dihedral_angle_4_deg19.553
r_dihedral_angle_3_deg12.072
r_dihedral_angle_1_deg5.755
r_angle_refined_deg1.556
r_mcangle_it1.409
r_mcbond_it0.869
r_angle_other_deg0.859
r_mcbond_other0.856
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4556
Nucleic Acid Atoms
Solvent Atoms711
Heterogen Atoms18

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
XDSdata reduction