X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KM3PDB entry 3km3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290Internal tracking number 225926. JCSG+ well A2. 20.0% w/v PEG3000, 0.1M Ammonium citrate/citric acid, 20% Ethylene glycol Cryo. ButhA.00973.a.A1 PS01180 46.83mg/ml, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.6553.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.87α = 90
b = 92.87β = 90
c = 137.59γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focus K-B pair Si plus Pt, Rh coatings2011-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
12.0569.441000.04422.714.522777227763-339.228
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)
12.052.11000.4583.44.482046

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 DIFFRACTIONMRTHROUGHOUTPDB entry 3km32.0569.442777227761139599.960.1680.1680.1680.186RANDOM39.189
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]
0.360.180.36-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.348
r_dihedral_angle_4_deg19.154
r_dihedral_angle_3_deg13.325
r_dihedral_angle_1_deg6.056
r_angle_refined_deg1.417
r_angle_other_deg1.018
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.348
r_dihedral_angle_4_deg19.154
r_dihedral_angle_3_deg13.325
r_dihedral_angle_1_deg6.056
r_angle_refined_deg1.417
r_angle_other_deg1.018
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2535
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms28

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction