X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X1Lpdb entry 2x1l

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289BrabA.10201.a.A1 PW27667 at 28.7 mg/mL with 5 mM selenomethionine and 5 mM ATP against JCSG+ screen condition C3, 0.2 M ammonium nitrate, 20% PEG 3350, crystal tracking ID 226820c3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5251.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.25α = 90
b = 77.62β = 119.67
c = 116.27γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.655099.30.07115.213.75272452379-351.6
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)
12.652.7299.50.4862.63

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 REPLACEMENTTHROUGHOUTpdb entry 2x1l2.655052379267199.60.19910.19710.2373RANDOM48.2529
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]
-2.33-1.213.8-2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.969
r_dihedral_angle_4_deg18.08
r_dihedral_angle_3_deg13.16
r_dihedral_angle_1_deg5.652
r_angle_refined_deg1.421
r_angle_other_deg1.149
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.969
r_dihedral_angle_4_deg18.08
r_dihedral_angle_3_deg13.16
r_dihedral_angle_1_deg5.652
r_angle_refined_deg1.421
r_angle_other_deg1.149
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10934
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms27

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction