X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6II6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27712% PEG 3000, 0.1M Na2HPO4/citric acid (pH 4.2), 0.4M NaCl, 10% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.64α = 90
b = 78.64β = 90
c = 450.008γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702018-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.9793PAL/PLS7A (6B, 6C1)

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
12.365097.36.1560806
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.362.40.6430.2730.77

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 REPLACEMENTTHROUGHOUT6II62.365059323319397.280.185170.182420.23662RANDOM39.146
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]
0.110.060.11-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.163
r_dihedral_angle_4_deg18.791
r_dihedral_angle_3_deg15.994
r_long_range_B_refined9.411
r_long_range_B_other9.41
r_dihedral_angle_1_deg7.167
r_scangle_other6.557
r_mcangle_it5.681
r_mcangle_other5.68
r_scbond_it4.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.163
r_dihedral_angle_4_deg18.791
r_dihedral_angle_3_deg15.994
r_long_range_B_refined9.411
r_long_range_B_other9.41
r_dihedral_angle_1_deg7.167
r_scangle_other6.557
r_mcangle_it5.681
r_mcangle_other5.68
r_scbond_it4.356
r_scbond_other4.354
r_mcbond_it3.631
r_mcbond_other3.63
r_angle_refined_deg1.436
r_angle_other_deg0.83
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.002
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 Atoms9567
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
REFMACrefinement