8Z2B | pdb_00008z2b

Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XVI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.2 M MgCl2, 0.1 M Tris pH 7, and 10% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.69	α = 90
b = 101.69	β = 90
c = 271.68	γ = 120

Symmetry
Space Group	P 32

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++		2017-08-17	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)	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	2.85	30	99.9	0.98	9.3	5.65		73339

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	2.85	2.95			0.61

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5XVI	2.85	29.89	69568	3769	99.955	0.196	0.1919	0.1971	0.2677	0.2592	47.117

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]
-5.363			-5.363		10.725

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.858
r_dihedral_angle_6_deg	14.418
r_lrange_it	13.355
r_lrange_other	13.354
r_dihedral_angle_2_deg	9.258
r_dihedral_angle_1_deg	7.835
r_mcangle_it	6.666
r_mcangle_other	6.666
r_scangle_it	5.396
r_scangle_other	5.396
r_mcbond_it	4.032
r_mcbond_other	4.032
r_scbond_it	3.145
r_scbond_other	3.145
r_angle_refined_deg	1.654
r_symmetry_xyhbond_nbd_refined	0.713
r_angle_other_deg	0.585
r_symmetry_nbd_refined	0.493
r_nbd_other	0.409
r_xyhbond_nbd_other	0.247
r_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.215
r_ncsr_local_group_3	0.212
r_ncsr_local_group_14	0.212
r_ncsr_local_group_13	0.211
r_nbd_refined	0.209
r_ncsr_local_group_11	0.209
r_ncsr_local_group_10	0.208
r_ncsr_local_group_4	0.207
r_ncsr_local_group_15	0.207
r_ncsr_local_group_7	0.206
r_ncsr_local_group_8	0.205
r_ncsr_local_group_2	0.2
r_ncsr_local_group_12	0.2
r_ncsr_local_group_9	0.199
r_ncsr_local_group_6	0.198
r_ncsr_local_group_5	0.197
r_ncsr_local_group_1	0.191
r_nbtor_refined	0.177
r_chiral_restr	0.087
r_symmetry_xyhbond_nbd_other	0.086
r_symmetry_nbtor_other	0.084
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20802
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms

Software

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