X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D3A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol (racemic), 20 mM 2-Propanol, 20 mM 1,4-Butanediol, 20 mM 1,3-Propanediol, 100 mM Imidazole-MES pH 6.5, 30% Glycerol and 30% polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
2.5351.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.038α = 90
b = 101.162β = 90
c = 143.214γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.7546.6199.30.99813.8792027
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)
11.751.77920.922.66.8

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 REPLACEMENTTHROUGHOUT3D3A1.7546.6187417454499.570.157370.156240.17846RANDOM17.784
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]
0.020.08-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.26
r_dihedral_angle_4_deg14.094
r_dihedral_angle_3_deg11.545
r_dihedral_angle_1_deg6.495
r_long_range_B_refined4.206
r_long_range_B_other4.206
r_scangle_other2.858
r_mcangle_it1.785
r_mcangle_other1.785
r_scbond_it1.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.26
r_dihedral_angle_4_deg14.094
r_dihedral_angle_3_deg11.545
r_dihedral_angle_1_deg6.495
r_long_range_B_refined4.206
r_long_range_B_other4.206
r_scangle_other2.858
r_mcangle_it1.785
r_mcangle_other1.785
r_scbond_it1.753
r_scbond_other1.753
r_angle_refined_deg1.431
r_mcbond_it1.117
r_mcbond_other1.116
r_angle_other_deg0.92
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms6069
Nucleic Acid Atoms
Solvent Atoms625
Heterogen Atoms13

Software

Software
Software NamePurpose
GDAdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement