6CZL

Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32922.63 M NaCl, 100 mM Bis-Tris propane pH 6.3
Crystal Properties
Matthews coefficientSolvent content
4.2170.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.826α = 90
b = 195.621β = 95.85
c = 100.209γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.9780APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.925099.10.0670.07615.24.282460
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.923.0995.30.91.051.83.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.9239.1781223123799.150.1980.1970.25RANDOM100.861
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]
1.020.16-0.98-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.253
r_dihedral_angle_3_deg16.676
r_dihedral_angle_4_deg12.995
r_dihedral_angle_1_deg7.07
r_long_range_B_refined5.868
r_long_range_B_other5.867
r_mcangle_it3.731
r_mcangle_other3.73
r_scangle_other3.241
r_mcbond_it2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.253
r_dihedral_angle_3_deg16.676
r_dihedral_angle_4_deg12.995
r_dihedral_angle_1_deg7.07
r_long_range_B_refined5.868
r_long_range_B_other5.867
r_mcangle_it3.731
r_mcangle_other3.73
r_scangle_other3.241
r_mcbond_it2.07
r_mcbond_other2.07
r_scbond_it1.761
r_scbond_other1.761
r_angle_refined_deg1.286
r_angle_other_deg0.914
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms15480
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing