X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B7WPDB ENTRY 3B7W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2M AM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.32α = 90
b = 98.32β = 90
c = 381.44γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISOSMIC2008-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.638.9296.70.1910.13.9545072
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)
12.62.67900.472.33.2

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 3B7W2.638.9254057284296.70.2360.2350.255RANDOM13.29
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]
-0.62-0.621.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.707
r_dihedral_angle_4_deg16.083
r_dihedral_angle_3_deg15.186
r_dihedral_angle_1_deg5.772
r_scangle_it3.515
r_scbond_it2.395
r_angle_other_deg2.199
r_mcangle_it1.396
r_angle_refined_deg1.232
r_mcbond_it0.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.707
r_dihedral_angle_4_deg16.083
r_dihedral_angle_3_deg15.186
r_dihedral_angle_1_deg5.772
r_scangle_it3.515
r_scbond_it2.395
r_angle_other_deg2.199
r_mcangle_it1.396
r_angle_refined_deg1.232
r_mcbond_it0.807
r_mcbond_other0.108
r_chiral_restr0.065
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12363
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing