X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EYWPDB ENTRY 3EYW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52989% PEG 3350, 100mM ammonium sulfate, 100mM Bis-Tris buffer, 50mM magnesium formate, 1mM NAD+, pH 5.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8456.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.949α = 90
b = 85.941β = 90
c = 189.408γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
12.15098.50.0917.84.762001
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)
2.12.18910.444

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 3EYW2.138.2658735311098.540.204450.202810.23567RANDOM29.692
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]
-11.85-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.604
r_dihedral_angle_4_deg20.666
r_dihedral_angle_3_deg15.1
r_dihedral_angle_1_deg5.868
r_scangle_it3.967
r_scbond_it2.581
r_mcangle_it1.714
r_angle_refined_deg1.449
r_mcbond_it1.113
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.604
r_dihedral_angle_4_deg20.666
r_dihedral_angle_3_deg15.1
r_dihedral_angle_1_deg5.868
r_scangle_it3.967
r_scbond_it2.581
r_mcangle_it1.714
r_angle_refined_deg1.449
r_mcbond_it1.113
r_nbtor_refined0.308
r_nbd_refined0.207
r_symmetry_vdw_refined0.203
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.143
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.006
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_refined
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 Atoms5398
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms132

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction