X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1URKPDB ENTRY 1URK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10.52931.2 M sodium dihydrogen phosphate, 0.8 M potassium hydrogen phosphate, 200 mM lithium sulfate, 100 mM CHES, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8556.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.603α = 107.62
b = 64.327β = 92.11
c = 64.623γ = 95.75
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 225 mm2005-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.13539APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.94096.40.04519.633.85465054650-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.97870.2212.582.84899

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 1URK1.91551775275796.140.18290.181530.20822RANDOM29.676
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]
0.170.6-0.750.02-0.46-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.287
r_dihedral_angle_4_deg16.955
r_dihedral_angle_3_deg13.186
r_dihedral_angle_1_deg6.336
r_scangle_it3.81
r_scbond_it2.534
r_mcangle_it1.544
r_angle_refined_deg1.489
r_mcbond_it0.945
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.287
r_dihedral_angle_4_deg16.955
r_dihedral_angle_3_deg13.186
r_dihedral_angle_1_deg6.336
r_scangle_it3.81
r_scbond_it2.534
r_mcangle_it1.544
r_angle_refined_deg1.489
r_mcbond_it0.945
r_nbtor_refined0.304
r_symmetry_vdw_refined0.22
r_nbd_refined0.197
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.125
r_chiral_restr0.115
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 Atoms3897
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing