5O9Y

Crystal structure of ScGas2 in complex with compound 11


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W62 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3500, ammonium sulfate, BIS-Tris pH 6
Crystal Properties
Matthews coefficientSolvent content
2.1141.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.92α = 90
b = 70.38β = 90
c = 150.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.57150.0794.90.07613.49.170765
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.6573.90.7122.58

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 REPLACEMENTTHROUGHOUT2W621.57150.0768554213594.620.22110.220730.23306RANDOM24.923
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]
-0.70.89-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.52
r_dihedral_angle_4_deg13.594
r_dihedral_angle_3_deg11.862
r_dihedral_angle_1_deg5.851
r_long_range_B_refined3.341
r_long_range_B_other3.341
r_mcangle_it1.166
r_mcangle_other1.165
r_angle_refined_deg1.122
r_scangle_other0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.52
r_dihedral_angle_4_deg13.594
r_dihedral_angle_3_deg11.862
r_dihedral_angle_1_deg5.851
r_long_range_B_refined3.341
r_long_range_B_other3.341
r_mcangle_it1.166
r_mcangle_other1.165
r_angle_refined_deg1.122
r_scangle_other0.97
r_angle_other_deg0.913
r_mcbond_it0.634
r_mcbond_other0.634
r_scbond_it0.556
r_scbond_other0.556
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms3423
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing