5XWC

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	40% v/v PEG 300, 0.1M sodium cacodylate, pH 6.5, 0.2 M calcium acetate hydrate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.41	α = 90
b = 173.41	β = 90
c = 241.83	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2016-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	35	99	0.11	13.4	7.9		138857

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85	99.9		0.69	1.9	7.9

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	1.75	34	131488	6920	98.95	0.15613	0.15545	0.16921	RANDOM	28.291

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]
0.08	0.04		0.08		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.459
r_dihedral_angle_4_deg	16.218
r_dihedral_angle_3_deg	11.976
r_long_range_B_refined	7.923
r_long_range_B_other	7.227
r_dihedral_angle_1_deg	5.822
r_scangle_other	3.928
r_scbond_it	2.628
r_scbond_other	2.628
r_mcangle_other	1.957
r_mcangle_it	1.956
r_angle_refined_deg	1.654
r_mcbond_it	1.366
r_mcbond_other	1.362
r_angle_other_deg	0.992
r_chiral_restr	0.201
r_bond_refined_d	0.012
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
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	3469
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	370

Software

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