X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 184L 

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
2.7955.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.487α = 90
b = 60.487β = 90
c = 97.136γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV2006-10-25MSINGLE 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
11.5652.4199.40.07414.85.22977429774
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)
1.561.621000.6325.42936

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 DIFFRACTIONTHROUGHOUT184L1.752.412306623066114399.240.1930.1930.1910.23RANDOM18.094
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]
0.440.220.44-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.406
r_dihedral_angle_4_deg19.99
r_dihedral_angle_3_deg11.74
r_dihedral_angle_1_deg5.897
r_scangle_it3.064
r_scbond_it2.105
r_angle_refined_deg1.234
r_mcangle_it1.052
r_mcbond_it0.682
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.406
r_dihedral_angle_4_deg19.99
r_dihedral_angle_3_deg11.74
r_dihedral_angle_1_deg5.897
r_scangle_it3.064
r_scbond_it2.105
r_angle_refined_deg1.234
r_mcangle_it1.052
r_mcbond_it0.682
r_nbtor_refined0.303
r_symmetry_vdw_refined0.236
r_nbd_refined0.203
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.142
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1308
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms25

Software

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