X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X1SPDB ENTRY 1X1S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2293Ammonium sulfate, sodium acetate, PEG-4000, glycerol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5952.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.196α = 90
b = 192.248β = 90
c = 43.235γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2008-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.949.5799.20.0990.0993.86.45212952129
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9294.80.2820.2822.54.17118

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1X1S1.949.574940349403264999.180.185840.185840.183920.22192RANDOM24.125
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.877
r_dihedral_angle_4_deg19.483
r_dihedral_angle_3_deg12.996
r_dihedral_angle_1_deg5.395
r_scangle_it2.679
r_scbond_it1.677
r_angle_refined_deg1.198
r_mcangle_it1.157
r_mcbond_it0.732
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.877
r_dihedral_angle_4_deg19.483
r_dihedral_angle_3_deg12.996
r_dihedral_angle_1_deg5.395
r_scangle_it2.679
r_scbond_it1.677
r_angle_refined_deg1.198
r_mcangle_it1.157
r_mcbond_it0.732
r_nbtor_refined0.303
r_symmetry_vdw_refined0.208
r_nbd_refined0.188
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.135
r_chiral_restr0.078
r_metal_ion_refined0.039
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4138
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms114

Software

Software
Software NamePurpose
BSSdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling