5VLC

Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2292100 mM MES pH 5.2, 200 mM NACl, 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2244.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.859α = 90
b = 139.201β = 119.18
c = 102.692γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97625APS22-ID

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
11.9748.7399.40.07813.76.14175983
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)
11.972.0997.40.9051.95.7

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 REPLACEMENTFREE R-VALUE1kae1.9748.73174751123299.570.178880.178530.22912RANDOM47.206
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]
0.050.22-0.380.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.009
r_dihedral_angle_3_deg15.111
r_dihedral_angle_4_deg14.857
r_dihedral_angle_1_deg6.321
r_long_range_B_refined5.519
r_long_range_B_other5.494
r_scangle_other3.536
r_mcangle_it2.811
r_mcangle_other2.811
r_scbond_it2.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.009
r_dihedral_angle_3_deg15.111
r_dihedral_angle_4_deg14.857
r_dihedral_angle_1_deg6.321
r_long_range_B_refined5.519
r_long_range_B_other5.494
r_scangle_other3.536
r_mcangle_it2.811
r_mcangle_other2.811
r_scbond_it2.167
r_scbond_other2.167
r_mcbond_it1.791
r_mcbond_other1.791
r_angle_refined_deg1.693
r_angle_other_deg1.014
r_chiral_restr0.103
r_bond_refined_d0.015
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other
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 Atoms19688
Nucleic Acid Atoms
Solvent Atoms625
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing