X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.1530% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCl, pH8.5
Crystal Properties
Matthews coefficientSolvent content
2.4750.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.413α = 90
b = 40.69β = 89.99
c = 61.147γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray101CCDAGILENT EOS CCD2010-10-25MSINGLE 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)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
1161.1599.56.326.467481
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)
111.0499.90.2890.2896.326.4

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 REPLACEMENTTHROUGHOUT2ZVX1.1261.1561177327495.450.131260.130480.14575RANDOM8.304
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]
0.07-0.14-0.05-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.759
r_dihedral_angle_2_deg21.182
r_sphericity_bonded11.547
r_dihedral_angle_4_deg9.717
r_dihedral_angle_3_deg9.528
r_rigid_bond_restr6.843
r_dihedral_angle_1_deg6.572
r_long_range_B_refined4.157
r_angle_refined_deg2.988
r_long_range_B_other2.513
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.759
r_dihedral_angle_2_deg21.182
r_sphericity_bonded11.547
r_dihedral_angle_4_deg9.717
r_dihedral_angle_3_deg9.528
r_rigid_bond_restr6.843
r_dihedral_angle_1_deg6.572
r_long_range_B_refined4.157
r_angle_refined_deg2.988
r_long_range_B_other2.513
r_scbond_it1.765
r_scbond_other1.764
r_scangle_other1.576
r_angle_other_deg0.995
r_mcangle_it0.788
r_mcangle_other0.788
r_mcbond_other0.683
r_mcbond_it0.68
r_chiral_restr0.185
r_bond_refined_d0.038
r_gen_planes_refined0.012
r_bond_other_d0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms902
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms30

Software

Software
Software NamePurpose
SHELXLdata collection
DENZOdata reduction
SCALAdata scaling
REFMACrefinement