5XVX

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-ketoglutarate and NADPH

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	0.1 M sodium citrate (pH 5.5), 20% (w/v) PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
7.12	82.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.46	α = 90
b = 174.46	β = 90
c = 240.43	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		2014-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9763	ESRF	BM14

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	1.8	35	99.6	0.092	0.99	17.08	12.2		128967

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	1.8	1.9	97.9		0.41	0.96	5.1	10.9

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	1.8	34	122517	6448	99.65	0.13582	0.13518	0.14799	RANDOM	29.177

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]
0.21	0.11		0.21		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.899
r_dihedral_angle_4_deg	16.9
r_dihedral_angle_3_deg	11.931
r_long_range_B_refined	9.045
r_long_range_B_other	7.673
r_dihedral_angle_1_deg	5.98
r_scangle_other	3.932
r_scbond_it	2.661
r_scbond_other	2.654
r_mcangle_other	2.235
r_mcangle_it	2.233
r_mcbond_it	1.667
r_mcbond_other	1.661
r_angle_refined_deg	1.654
r_angle_other_deg	0.979
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.006
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	3473
Nucleic Acid Atoms
Solvent Atoms	674
Heterogen Atoms	210

Software

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