X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YLJPDB ENTRY 1YLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.7292Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0239.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.279α = 90
b = 106.765β = 101.74
c = 47.777γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM Q315rMIRRORS2008-04-11SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.75098.60.10310.8173.548267-3
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)
1.71.7687.10.42.9

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 1YLJ1.746.7848236244398.90.170.1680.203RANDOM15.81
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]
-0.021.4-0.441.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.194
r_dihedral_angle_4_deg13.557
r_dihedral_angle_3_deg12.329
r_dihedral_angle_1_deg5.91
r_scangle_it3.051
r_scbond_it1.968
r_angle_refined_deg1.668
r_mcangle_it1.149
r_mcbond_it0.714
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.194
r_dihedral_angle_4_deg13.557
r_dihedral_angle_3_deg12.329
r_dihedral_angle_1_deg5.91
r_scangle_it3.051
r_scbond_it1.968
r_angle_refined_deg1.668
r_mcangle_it1.149
r_mcbond_it0.714
r_nbtor_refined0.3
r_nbd_refined0.199
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.118
r_chiral_restr0.106
r_symmetry_hbond_refined0.094
r_bond_refined_d0.012
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 Atoms3952
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms107

Software

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