X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2289MythA00185bA1 PS00649 116 mg/mL grown against JCSG+ C1 0.2 M NaCl, 0.1 M phosphate citrate pH 4.2, 20% PEG 8000 and soaked for 20 minutes against 15% PEG 8000, 25% PEG 400, 1 M NaI, 0.1 M phosphate citrate pH 4.2, crystal tracking ID 216661c1-1MNaI, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3547.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.43α = 90
b = 114.55β = 92.13
c = 92.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442010-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.15099.30.13211.747.289991-324.921
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)
12.12.1591.20.5313.56.26704

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 DIFFRACTIONSAD WITH MRTHROUGHOUT1jqi2.15089872450799.180.1710.16910.2068RANDOM21.3214
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]
-0.57-0.36-0.090.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg17.561
r_dihedral_angle_3_deg13.581
r_dihedral_angle_1_deg5.346
r_scangle_it3.262
r_scbond_it2.033
r_angle_refined_deg1.393
r_mcangle_it1.17
r_mcbond_it0.664
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg17.561
r_dihedral_angle_3_deg13.581
r_dihedral_angle_1_deg5.346
r_scangle_it3.262
r_scbond_it2.033
r_angle_refined_deg1.393
r_mcangle_it1.17
r_mcbond_it0.664
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10870
Nucleic Acid Atoms
Solvent Atoms623
Heterogen Atoms321

Software

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