X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RGR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22981.6 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0239.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.514α = 90
b = 76.644β = 63.96
c = 53.06γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.980SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.46538.322980.038183.67716877168
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.5488.40.8720.8720.93.210103

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT3RGR1.4738.3217710877108385297.970.18760.18760.18590.2181RANDOM27.0688
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]
-0.1-0.180.8-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_3_deg15.354
r_dihedral_angle_4_deg14.645
r_dihedral_angle_1_deg6.12
r_scangle_it3.719
r_scbond_it2.354
r_mcangle_it1.652
r_angle_refined_deg1.521
r_angle_other_deg0.934
r_mcbond_it0.934
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_3_deg15.354
r_dihedral_angle_4_deg14.645
r_dihedral_angle_1_deg6.12
r_scangle_it3.719
r_scbond_it2.354
r_mcangle_it1.652
r_angle_refined_deg1.521
r_angle_other_deg0.934
r_mcbond_it0.934
r_mcbond_other0.256
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3955
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms45

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction