5XW0

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Isophthalate and NADPH

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	0.1 M MES (pH 6.0) 30% (v/v) PEG 200, 5 % (w/v) PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
7.06	82.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.48	α = 90
b = 173.48	β = 90
c = 241.14	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	1.9	70	99.9	0.054	0.99	24.3	7.4		109208

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	1.9	2	98.8		0.42	0.61	4.5	6.9

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	1.9	40	103738	5460	99.9	0.16867	0.16805	0.18038	RANDOM	31.006

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]
0.17	0.08		0.17		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.785
r_dihedral_angle_4_deg	18.212
r_dihedral_angle_3_deg	11.756
r_long_range_B_refined	5.939
r_dihedral_angle_1_deg	5.802
r_long_range_B_other	5.66
r_scangle_other	3.835
r_scbond_it	2.422
r_scbond_other	2.406
r_mcangle_other	2.401
r_mcangle_it	2.4
r_mcbond_it	1.663
r_mcbond_other	1.661
r_angle_refined_deg	1.444
r_angle_other_deg	0.95
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_bond_other_d	0.007
r_gen_planes_refined	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	307
Heterogen Atoms	166

Software

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