X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DX7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92900.05M ADA, pH 6.9, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 5-10% PEG4000, 0.004m FUSIDIC ACID
Crystal Properties
Matthews coefficientSolvent content
3.8467.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.654α = 90
b = 163.248β = 90
c = 246.042γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.349.1592.84.16.7259156
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)
12.32.381000.228.1

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 REPLACEMENTTHROUGHOUT4DX72.549.151921301011399.950.226680.224860.26147RANDOM63.517
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]
-4.154.55-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.018
r_dihedral_angle_4_deg13.667
r_dihedral_angle_3_deg12.779
r_dihedral_angle_1_deg5.025
r_long_range_B_refined4.818
r_long_range_B_other4.817
r_mcangle_it2.636
r_mcangle_other2.636
r_scangle_other2.539
r_mcbond_it1.512
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.018
r_dihedral_angle_4_deg13.667
r_dihedral_angle_3_deg12.779
r_dihedral_angle_1_deg5.025
r_long_range_B_refined4.818
r_long_range_B_other4.817
r_mcangle_it2.636
r_mcangle_other2.636
r_scangle_other2.539
r_mcbond_it1.512
r_mcbond_other1.512
r_scbond_it1.422
r_scbond_other1.422
r_angle_refined_deg1.105
r_angle_other_deg0.838
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25920
Nucleic Acid Atoms
Solvent Atoms815
Heterogen Atoms874

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing