X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DU8PDB ENTRY 2DU8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829310% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.661α = 90
b = 181.745β = 90
c = 50.717γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2006-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.0

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
13.25097.50.1337.23.723223
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)
13.23.3192.30.2233.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DU83.25021972118797.230.223960.223960.221110.2756RANDOM40.757
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]
3.96-6.92.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.678
r_dihedral_angle_3_deg19.143
r_dihedral_angle_4_deg19.091
r_dihedral_angle_1_deg4.843
r_scangle_it1.921
r_angle_refined_deg1.506
r_scbond_it1.413
r_mcangle_it1.136
r_mcbond_it0.719
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.678
r_dihedral_angle_3_deg19.143
r_dihedral_angle_4_deg19.091
r_dihedral_angle_1_deg4.843
r_scangle_it1.921
r_angle_refined_deg1.506
r_scbond_it1.413
r_mcangle_it1.136
r_mcbond_it0.719
r_nbtor_refined0.319
r_nbd_refined0.255
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.117
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.004
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 Atoms10932
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing