X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B1A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827740 mM sodium phosphate pH 6.8, 0.2% decylmaltoside, 1% polyethylene glycol 4000, 2% ethylene glycol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.998α = 90
b = 204.193β = 90
c = 177.759γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray60CCDRAYONIX MX225HE2012-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.32001000.030.5539.713.41596005
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.310.94

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 REPLACEMENTTHROUGHOUT5B1A1.34015108227918399.580.14960.14850.1704RANDOM30.499
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]
0.46-1.581.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.911
r_dihedral_angle_4_deg15.271
r_dihedral_angle_3_deg13.983
r_dihedral_angle_1_deg6.172
r_rigid_bond_restr5.786
r_angle_refined_deg2.27
r_angle_other_deg1.526
r_chiral_restr0.466
r_bond_refined_d0.021
r_gen_planes_refined0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.911
r_dihedral_angle_4_deg15.271
r_dihedral_angle_3_deg13.983
r_dihedral_angle_1_deg6.172
r_rigid_bond_restr5.786
r_angle_refined_deg2.27
r_angle_other_deg1.526
r_chiral_restr0.466
r_bond_refined_d0.021
r_gen_planes_refined0.015
r_gen_planes_other0.006
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms27834
Nucleic Acid Atoms
Solvent Atoms2080
Heterogen Atoms2608

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing