X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E6U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP282.150.7-0.75 M succinic acid pH 7.0, 0.1 M bis-tris propane pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.505α = 90
b = 121.134β = 90
c = 142.895γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002021-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.51292.4011000.0790.0820.0220.99920.614.4150903
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5121.5171001.0881.1420.3410.8132.110.7

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 REPLACEMENTTHROUGHOUT3E6U1.5225141284734799.970.173140.172140.19231RANDOM21.88
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]
-0.521.15-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.991
r_dihedral_angle_4_deg15.502
r_dihedral_angle_3_deg13.056
r_dihedral_angle_1_deg6.163
r_long_range_B_refined4.393
r_mcangle_it1.376
r_scbond_it1.365
r_angle_refined_deg1.02
r_mcbond_it0.822
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.991
r_dihedral_angle_4_deg15.502
r_dihedral_angle_3_deg13.056
r_dihedral_angle_1_deg6.163
r_long_range_B_refined4.393
r_mcangle_it1.376
r_scbond_it1.365
r_angle_refined_deg1.02
r_mcbond_it0.822
r_chiral_restr0.09
r_gen_planes_refined0.005
r_bond_refined_d0.003
r_bond_other_d
r_angle_other_deg
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_it
r_scangle_other
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 Atoms6406
Nucleic Acid Atoms
Solvent Atoms897
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing