4NYZ

The EMCV 3Dpol structure with altered motif A conformation at 2.15A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U091U09(THE HOMOLOGY MODEL HAS BEEN USED.)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527710%PEG6000 and 2.0M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5765.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.553α = 90
b = 122.553β = 90
c = 198.797γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

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
12.15104.398.40.110.0996.45546584049922
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)
12.152.2798.30.860.7718.75

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 REPLACEMENTTHROUGHOUT1U09(THE HOMOLOGY MODEL HAS BEEN USED.)2.15104.35465838457203697.730.230610.230610.229480.2522RANDOM40.315
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]
0.960.96-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.172
r_dihedral_angle_4_deg14.787
r_dihedral_angle_3_deg14.24
r_dihedral_angle_1_deg4.727
r_long_range_B_refined2.871
r_long_range_B_other2.871
r_mcangle_it0.976
r_mcangle_other0.976
r_angle_refined_deg0.877
r_scangle_other0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.172
r_dihedral_angle_4_deg14.787
r_dihedral_angle_3_deg14.24
r_dihedral_angle_1_deg4.727
r_long_range_B_refined2.871
r_long_range_B_other2.871
r_mcangle_it0.976
r_mcangle_other0.976
r_angle_refined_deg0.877
r_scangle_other0.75
r_angle_other_deg0.7
r_mcbond_it0.528
r_mcbond_other0.528
r_scbond_other0.414
r_scbond_it0.413
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.003
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 Atoms3680
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms17

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling