X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B3XPDB ENTRY 3B3X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.4pH 3.4
Crystal Properties
Matthews coefficientSolvent content
2.5350.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.988α = 90
b = 104.479β = 94.07
c = 63.74γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2932000-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLURE BEAMLINE DW32LUREDW32

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
11.652798.30.0614.73.8724362
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)
11.651.7497.30.52.53.8

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 3B3X1.6517.768715365798.30.190060.18890.2114RANDOM16.606
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.992
r_dihedral_angle_4_deg16.075
r_dihedral_angle_3_deg14.289
r_dihedral_angle_1_deg5.768
r_scangle_it2.429
r_scbond_it1.685
r_angle_refined_deg1.313
r_mcangle_it0.837
r_mcbond_it0.507
r_symmetry_hbond_refined0.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.992
r_dihedral_angle_4_deg16.075
r_dihedral_angle_3_deg14.289
r_dihedral_angle_1_deg5.768
r_scangle_it2.429
r_scbond_it1.685
r_angle_refined_deg1.313
r_mcangle_it0.837
r_mcbond_it0.507
r_symmetry_hbond_refined0.366
r_nbtor_refined0.299
r_symmetry_vdw_refined0.232
r_nbd_refined0.196
r_xyhbond_nbd_refined0.095
r_chiral_restr0.075
r_bond_refined_d0.009
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_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 Atoms3990
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling