X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G6APDB entries 3G6A, 1IJZ
experimental modelPDB 1IJZPDB entries 3G6A, 1IJZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.52930.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.565

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.54α = 90
b = 68.03β = 90
c = 182.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray115CCDRIGAKU SATURN 944VARIMAX HF2006-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
13.26391.50.1616.1613028-319.5
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)
13.23.3188.20.224.62.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 3G6A, 1IJZ3.21516206123625011000.2130.2130.26342RANDOM18.7
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]
-1.182.76-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.716
r_scangle_it26.417
r_dihedral_angle_4_deg20.4
r_scbond_it20.351
r_dihedral_angle_3_deg20.079
r_dihedral_angle_1_deg6.704
r_mcangle_it4.75
r_mcbond_it1.387
r_angle_refined_deg1.361
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.716
r_scangle_it26.417
r_dihedral_angle_4_deg20.4
r_scbond_it20.351
r_dihedral_angle_3_deg20.079
r_dihedral_angle_1_deg6.704
r_mcangle_it4.75
r_mcbond_it1.387
r_angle_refined_deg1.361
r_nbtor_refined0.315
r_symmetry_vdw_refined0.297
r_nbd_refined0.239
r_xyhbond_nbd_refined0.158
r_chiral_restr0.086
r_symmetry_hbond_refined0.074
r_bond_refined_d0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_refined
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 Atoms4054
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms5

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
d*TREKdata reduction