X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S3R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829520 %(w/v) PEG3350, 200 mM NaH2PO4, 250 mM NaCl, 20 mM Tris-HCl, protein concentration 13 mg/ml, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7555.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.132α = 76.11
b = 77.019β = 75.48
c = 128.403γ = 66.31
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirror2013-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
12.13594.30.05812.022.1138781138781-3-336.54
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)
12.12.296.40.3943.03

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4S3R2.134.23138780138780697094.330.22270.22270.22080.2584RANDOM39.119
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]
0.03-1-0.05-0.880.150.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_4_deg16.926
r_dihedral_angle_3_deg14.025
r_dihedral_angle_1_deg5.759
r_angle_refined_deg1.275
r_mcangle_it0.771
r_angle_other_deg0.769
r_mcbond_it0.436
r_mcbond_other0.436
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_4_deg16.926
r_dihedral_angle_3_deg14.025
r_dihedral_angle_1_deg5.759
r_angle_refined_deg1.275
r_mcangle_it0.771
r_angle_other_deg0.769
r_mcbond_it0.436
r_mcbond_other0.436
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16350
Nucleic Acid Atoms
Solvent Atoms467
Heterogen Atoms51

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
PHASERphasing