X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VCC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.5298PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.2645.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.37α = 90
b = 100.71β = 90
c = 129.22γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDMARMOSAIC 300 mm CCD2015-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.279.4399.40.9969.44.325852
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3299.70.5491.1

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 REPLACEMENTTHROUGHOUT5VCC2.279.4324498131899.160.241910.240010.27522RANDOM74.444
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]
1.851.56-3.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.666
r_dihedral_angle_4_deg20.326
r_dihedral_angle_3_deg17.981
r_long_range_B_refined10.188
r_dihedral_angle_1_deg5.939
r_mcangle_it4.592
r_scbond_it3.217
r_mcbond_it2.91
r_angle_refined_deg1.381
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.666
r_dihedral_angle_4_deg20.326
r_dihedral_angle_3_deg17.981
r_long_range_B_refined10.188
r_dihedral_angle_1_deg5.939
r_mcangle_it4.592
r_scbond_it3.217
r_mcbond_it2.91
r_angle_refined_deg1.381
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms3676
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing