X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZIB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42930.1 M sodium acetate, 0.25 M ammonium sulfate, 8% PEG 3350 The Crystal was soaked in crystallizaion solution containing 2mM CaCl2 and pH adjusted to 7.0 before data collection.
Crystal Properties
Matthews coefficientSolvent content
2.0439.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.952α = 90
b = 65.952β = 90
c = 49.794γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)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
11.0621.56799.70.0450.0450.04810.110.556672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.061.121000.2290.2290.2413.410.3

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 REPLACEMENTTHROUGHOUT2ZIB1.0619.0453860287399.650.155020.154010.17418RANDOM9.774
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_deg36.844
r_dihedral_angle_4_deg13.983
r_dihedral_angle_3_deg11.003
r_dihedral_angle_1_deg7.308
r_long_range_B_refined4.181
r_long_range_B_other3.571
r_angle_other_deg2.453
r_scangle_other2.374
r_angle_refined_deg1.931
r_scbond_it1.667
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.844
r_dihedral_angle_4_deg13.983
r_dihedral_angle_3_deg11.003
r_dihedral_angle_1_deg7.308
r_long_range_B_refined4.181
r_long_range_B_other3.571
r_angle_other_deg2.453
r_scangle_other2.374
r_angle_refined_deg1.931
r_scbond_it1.667
r_scbond_other1.667
r_mcangle_it1.382
r_mcangle_other1.381
r_mcbond_it0.929
r_mcbond_other0.908
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.001
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 Atoms983
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing