5XVV

Crystal Structure of Forward Inhibited Aspergillus niger Glutamate Dehydrogenase With Both Apo- and Alpha Ketoglutarate Bound Subunits

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.15 M potassium bromide, 20% w/v PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.26	α = 103.4
b = 92.15	β = 93.95
c = 111.06	γ = 120.36

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2015-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	35	95.5	0.095	0.99	7.96	2		135737

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.35	92		0.39	0.68	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.25	33	128936	6786	95.53	0.16029	0.15826	0.19863	RANDOM	25.927

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]
-0.2	-0.29	-0.37	-0.11	0.1	0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.369
r_dihedral_angle_4_deg	14.754
r_dihedral_angle_3_deg	14.635
r_dihedral_angle_1_deg	6.228
r_long_range_B_refined	5.961
r_long_range_B_other	5.953
r_scangle_other	3.198
r_mcangle_it	2.203
r_mcangle_other	2.203
r_scbond_it	2.036
r_scbond_other	2.036
r_angle_refined_deg	1.433
r_mcbond_it	1.355
r_mcbond_other	1.355
r_angle_other_deg	0.971
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	20806
Nucleic Acid Atoms
Solvent Atoms	1516
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing