X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O6S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.465α = 90
b = 68.901β = 90
c = 132.358γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A1.05EMBL/DESY, HAMBURGBW7A

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
11.72098.80.0572755828
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)
11.71.76950.275

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 REPLACEMENTTHROUGHOUT1O6S1.765.9452919281598.640.158740.1560.21106RANDOM10.319
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]
-0.04-0.910.95
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.029
r_dihedral_angle_1_deg4.41
r_scbond_it4.378
r_mcangle_it3.907
r_mcbond_it2.999
r_angle_refined_deg2.006
r_angle_other_deg1.68
r_nbd_other0.189
r_nbd_refined0.187
r_symmetry_vdw_refined0.187
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.029
r_dihedral_angle_1_deg4.41
r_scbond_it4.378
r_mcangle_it3.907
r_mcbond_it2.999
r_angle_refined_deg2.006
r_angle_other_deg1.68
r_nbd_other0.189
r_nbd_refined0.187
r_symmetry_vdw_refined0.187
r_symmetry_vdw_other0.176
r_chiral_restr0.154
r_metal_ion_refined0.149
r_symmetry_hbond_refined0.134
r_xyhbond_nbd_refined0.12
r_nbtor_other0.075
r_bond_refined_d0.025
r_bond_other_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.009
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4304
Nucleic Acid Atoms
Solvent Atoms736
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction