X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SMLPDB ENTRY 1SML

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.752811.8M ammonium sulfate, 0.1M Hepes pH 7.75, 1.5% V/V Peg 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.35α = 90
b = 105.35β = 90
c = 197.08γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.54179

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
11.919.5199.80.0710.0719.36.9488032
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)
1.9299.80.410.3572.26.7

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 1SML1.919.5148803261399.860.186040.184270.21821RANDOM19.42
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.505
r_dihedral_angle_4_deg20.571
r_dihedral_angle_3_deg13.848
r_dihedral_angle_1_deg6.281
r_sphericity_free5.769
r_scangle_it3.17
r_scbond_it2.132
r_angle_refined_deg1.495
r_mcangle_it1.304
r_mcbond_it0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.505
r_dihedral_angle_4_deg20.571
r_dihedral_angle_3_deg13.848
r_dihedral_angle_1_deg6.281
r_sphericity_free5.769
r_scangle_it3.17
r_scbond_it2.132
r_angle_refined_deg1.495
r_mcangle_it1.304
r_mcbond_it0.843
r_nbtor_refined0.302
r_nbd_refined0.276
r_symmetry_vdw_refined0.218
r_symmetry_hbond_refined0.156
r_xyhbond_nbd_refined0.154
r_chiral_restr0.093
r_metal_ion_refined0.049
r_bond_refined_d0.015
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_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_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4002
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms65

Software

Software
Software NamePurpose
XDSdata scaling
SCALAdata scaling
CCP4model building
REFMACrefinement
XDSdata reduction
CCP4data scaling
CCP4phasing