8Z2C | pdb_00008z2c

Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) with open and partially closed conformations (form I)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ECS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
3.86	67.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.12	α = 90
b = 156.12	β = 90
c = 106.07	γ = 120

Symmetry
Space Group	P 63

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++		2021-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.05	40	98.9	0.17	0.99	11.9	10.8		95195			26.24

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	2.05	2.15	92.3		0.58

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7ECS	2.05	29.77	87330	4670	99.99	0.1774	0.17601	0.2021	0.203	0.23	RANDOM	28.029

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]
1.94			1.94		-3.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.898
r_dihedral_angle_4_deg	17.354
r_dihedral_angle_3_deg	15.804
r_dihedral_angle_1_deg	7.269
r_long_range_B_refined	5.704
r_long_range_B_other	5.686
r_scangle_other	4.425
r_mcangle_it	3.727
r_mcangle_other	3.727
r_scbond_it	3.314
r_scbond_other	3.314
r_mcbond_it	2.957
r_mcbond_other	2.957
r_angle_refined_deg	1.763
r_angle_other_deg	1.434
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	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	6908
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	16

Software

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