X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IY8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289Emerald Wizard Full screen condition F6, 20% PEG 3000, 0.1 M Tris, 0.2 M CaCl2, 11.8 mg/mL protein, crystal ID 202293f6, 25% glycerol as cryo-protectant, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2144.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.69α = 90
b = 51.38β = 94.5
c = 118.84γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002009-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97933APS23-ID-D

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
12.452098.80.1357.9736246-332.734
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)
12.452.5199.50.5612.22654

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 REPLACEMENTTHROUGHOUT1IY82.4519.936246180898.780.1950.1920.247RANDOM25.165
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]
2.842.01-1.98-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.777
r_dihedral_angle_3_deg15.139
r_dihedral_angle_4_deg13.464
r_dihedral_angle_1_deg5.804
r_scangle_it2.213
r_scbond_it1.304
r_angle_refined_deg1.176
r_mcangle_it0.885
r_angle_other_deg0.872
r_mcbond_it0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.777
r_dihedral_angle_3_deg15.139
r_dihedral_angle_4_deg13.464
r_dihedral_angle_1_deg5.804
r_scangle_it2.213
r_scbond_it1.304
r_angle_refined_deg1.176
r_mcangle_it0.885
r_angle_other_deg0.872
r_mcbond_it0.47
r_mcbond_other0.072
r_chiral_restr0.062
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6983
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction