X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YV3PDB entry 1YV3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7278mixing 5 ul of protein with an equal volume of well solution containing 100 mM MOPS, 250 mM MgCl2, 12% PEG 8000, 1 mM TCEP, and 2 mM Thymol, pH 7.0, vapor diffusion, hanging drop, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.8857.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.682α = 90
b = 146.317β = 90
c = 154.061γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID1.0APS32-ID

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
12.15098.40.06710.15.657739
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)
2.12.1898.80.2725.5

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 REPLACEMENTTHROUGHOUTPDB entry 1YV32.15054815291998.360.192920.190590.23773RANDOM28.502
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]
1.08-0.27-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.508
r_dihedral_angle_4_deg16.326
r_dihedral_angle_3_deg13.862
r_dihedral_angle_1_deg6.013
r_scangle_it3.778
r_scbond_it2.652
r_mcangle_it1.73
r_angle_refined_deg1.605
r_mcbond_it1.1
r_symmetry_vdw_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.508
r_dihedral_angle_4_deg16.326
r_dihedral_angle_3_deg13.862
r_dihedral_angle_1_deg6.013
r_scangle_it3.778
r_scbond_it2.652
r_mcangle_it1.73
r_angle_refined_deg1.605
r_mcbond_it1.1
r_symmetry_vdw_refined0.327
r_nbtor_refined0.306
r_symmetry_hbond_refined0.247
r_nbd_refined0.204
r_xyhbond_nbd_refined0.171
r_chiral_restr0.109
r_metal_ion_refined0.098
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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 Atoms5584
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms59

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling