X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DR2PDB ENTRY 2dr2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.2 M Sodium Malonate, 20% PEG 3350, 1mM TCEP, pH 7.0, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.294α = 95.29
b = 51.426β = 100.14
c = 89.97γ = 106.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-10-15SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.830.7697.10.0779.23.072057676
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)
12.82.995.70.3242.63.082053

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 2dr22.830.7620555106596.950.2440.2410.301RANDOM5.391
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]
-0.331.180.911.211.930.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.38
r_dihedral_angle_4_deg18.535
r_dihedral_angle_3_deg18.491
r_dihedral_angle_1_deg7.046
r_scangle_it1.547
r_angle_refined_deg1.238
r_scbond_it0.933
r_angle_other_deg0.922
r_mcangle_it0.686
r_mcbond_it0.367
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.38
r_dihedral_angle_4_deg18.535
r_dihedral_angle_3_deg18.491
r_dihedral_angle_1_deg7.046
r_scangle_it1.547
r_angle_refined_deg1.238
r_scbond_it0.933
r_angle_other_deg0.922
r_mcangle_it0.686
r_mcbond_it0.367
r_chiral_restr0.083
r_mcbond_other0.06
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5199
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
BALBESphasing