X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WRZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18%PEG 8000. Obtained crystal was soaked into a solution containing 100 mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate, 90mM NaCl, 10mM CsCl and 18% PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.308α = 90
b = 115.308β = 90
c = 67.475γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002013-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSAGA-LS BEAMLINE BL071.000, 2.166SAGA-LSBL07

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
12.15093.70.0798.73.25817729.6
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)
12.12.2391.50.4091.94

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 REPLACEMENTTHROUGHOUT3WRZ2.17.554284286797.650.14540.14380.17442RANDOM28.897
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]
-0.04-0.02-0.040.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg14.789
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg5.978
r_long_range_B_refined5.853
r_long_range_B_other5.788
r_scangle_other3.69
r_mcangle_it3.078
r_mcangle_other3.077
r_scbond_it2.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg14.789
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg5.978
r_long_range_B_refined5.853
r_long_range_B_other5.788
r_scangle_other3.69
r_mcangle_it3.078
r_mcangle_other3.077
r_scbond_it2.535
r_scbond_other2.534
r_mcbond_it2.191
r_mcbond_other2.191
r_angle_refined_deg1.365
r_angle_other_deg0.8
r_chiral_restr0.073
r_bond_refined_d0.011
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8186
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms11

Software

Software
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing