X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O5N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
3.3663.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.612α = 90
b = 100.612β = 90
c = 385.648γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.85099.60.080.02139.917.170033
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8695.50.450.120.952.511.8

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 REPLACEMENTTHROUGHOUT4O5N1.85066368348499.440.16590.164680.18896RANDOM33.169
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]
0.570.280.57-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_4_deg18.66
r_dihedral_angle_3_deg14.265
r_long_range_B_refined6.486
r_dihedral_angle_1_deg6.242
r_long_range_B_other5.847
r_scangle_other2.764
r_angle_refined_deg1.622
r_scbond_it1.586
r_scbond_other1.585
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_4_deg18.66
r_dihedral_angle_3_deg14.265
r_long_range_B_refined6.486
r_dihedral_angle_1_deg6.242
r_long_range_B_other5.847
r_scangle_other2.764
r_angle_refined_deg1.622
r_scbond_it1.586
r_scbond_other1.585
r_mcangle_it1.341
r_mcangle_other1.341
r_angle_other_deg0.98
r_mcbond_it0.785
r_mcbond_other0.785
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms3870
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms233

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing