4NTM

QueD soaked with sepiapterin (selenomethionine substituted protein)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62954% PEG 4000, 0.1 M sodium acetate soaked 1 hour with 7mM sepiapterin 17% PEG8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3347.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.297α = 90
b = 111.297β = 90
c = 126.047γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.000SSRLBL9-2

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
11.9391000.04323.27.26335663356
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)
11.921000.0113527.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0533.925946447712254499.510.226040.22450.25465RANDOM60.868
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]
0.850.85-1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.236
r_dihedral_angle_4_deg14.542
r_dihedral_angle_3_deg14.205
r_long_range_B_refined6.221
r_long_range_B_other6.21
r_dihedral_angle_1_deg5.742
r_scbond_other2.253
r_scangle_other1.904
r_scbond_it1.71
r_mcangle_other1.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.236
r_dihedral_angle_4_deg14.542
r_dihedral_angle_3_deg14.205
r_long_range_B_refined6.221
r_long_range_B_other6.21
r_dihedral_angle_1_deg5.742
r_scbond_other2.253
r_scangle_other1.904
r_scbond_it1.71
r_mcangle_other1.614
r_angle_refined_deg1.135
r_mcangle_it0.902
r_angle_other_deg0.737
r_mcbond_it0.515
r_mcbond_other0.515
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms5644
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms96

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling