X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LGU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7855.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.362α = 90
b = 60.362β = 90
c = 97.368γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2007-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.63352.2796.80.06412.83.52533625336
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)
1.6331.6993.20.4513.72368

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 DIFFRACTIONTHROUGHOUT1LGU1.63352.2725310253101276970.2090.2090.2080.24RANDOM20.494
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]
0.470.240.47-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.556
r_dihedral_angle_4_deg12.401
r_dihedral_angle_3_deg12.346
r_sphericity_free5.407
r_dihedral_angle_1_deg5.252
r_sphericity_bonded3.644
r_scangle_it3.625
r_scbond_it2.675
r_mcangle_it1.601
r_rigid_bond_restr1.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.556
r_dihedral_angle_4_deg12.401
r_dihedral_angle_3_deg12.346
r_sphericity_free5.407
r_dihedral_angle_1_deg5.252
r_sphericity_bonded3.644
r_scangle_it3.625
r_scbond_it2.675
r_mcangle_it1.601
r_rigid_bond_restr1.594
r_angle_refined_deg1.283
r_mcbond_it1.165
r_nbtor_refined0.303
r_nbd_refined0.208
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.138
r_chiral_restr0.078
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1309
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms16

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACphasing