X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B2X2B2X,1LVE
experimental modelPDB 1LVE2B2X,1LVE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52932.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8757

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.71α = 90
b = 111β = 90
c = 159.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU SATURN 944VARIMAX HF2008-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
123099.70.09421.611.675540-329.4
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)
122.0696.90.48859.2

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 REPLACEMENTTHROUGHOUT2B2X,1LVE21574238110998.20.216320.215780.25132RANDOM46.4
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]
0.94-0.23-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.345
r_scangle_it24.83
r_dihedral_angle_4_deg23.87
r_scbond_it23.763
r_dihedral_angle_3_deg13.55
r_dihedral_angle_1_deg5.897
r_mcangle_it4.752
r_mcbond_it2.812
r_angle_refined_deg1.148
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.345
r_scangle_it24.83
r_dihedral_angle_4_deg23.87
r_scbond_it23.763
r_dihedral_angle_3_deg13.55
r_dihedral_angle_1_deg5.897
r_mcangle_it4.752
r_mcbond_it2.812
r_angle_refined_deg1.148
r_chiral_restr0.071
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_refined
r_gen_planes_other
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_mcbond_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 Atoms6548
Nucleic Acid Atoms
Solvent Atoms635
Heterogen Atoms15

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement