X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IOCPDB ENTRY 2IOC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29322% PEG 3350, 50mM MES, pH 6.5, 50mM HEPES, pH 7.15, 2mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.85α = 90
b = 57.141β = 107.47
c = 68.47γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUmirrors2006-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.161.8699.90.0511.23.513789937899
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)
12.112.2299.90.2314.13.553936

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 2IOC2.161.926646140199.690.195140.19190.25916RANDOM41.719
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]
-3.35-1.133.46-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.818
r_dihedral_angle_4_deg20.968
r_dihedral_angle_3_deg17.764
r_dihedral_angle_1_deg7.241
r_scangle_it3.513
r_scbond_it2.429
r_angle_refined_deg1.952
r_mcangle_it1.543
r_mcbond_it0.987
r_symmetry_hbond_refined0.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.818
r_dihedral_angle_4_deg20.968
r_dihedral_angle_3_deg17.764
r_dihedral_angle_1_deg7.241
r_scangle_it3.513
r_scbond_it2.429
r_angle_refined_deg1.952
r_mcangle_it1.543
r_mcbond_it0.987
r_symmetry_hbond_refined0.456
r_nbtor_refined0.304
r_metal_ion_refined0.267
r_symmetry_vdw_refined0.234
r_nbd_refined0.228
r_xyhbond_nbd_refined0.211
r_chiral_restr0.137
r_bond_refined_d0.02
r_gen_planes_refined0.008
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_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3437
Nucleic Acid Atoms162
Solvent Atoms288
Heterogen Atoms4

Software

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