Experiment: 8AR8

Bovine glutamate dehydrogenase in complex with ADP at 2.4 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3JCZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20 mM CaCl2, 100 mM Na-acetate buffer (pH 4.6), 30% MPD (2-methyl-2,4-pentanediol)

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.51	α = 99.35
b = 92.03	β = 106.73
c = 119.57	γ = 109.73

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2021-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.97625	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.4	47.458	89.9	0.175	0.925	5	3.4		96056

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.484	86		0.398	0.668	2	3.6

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	3JCZ	2.4	47.46	96056	4664	76.3	0.2052	0.2037	0.198	0.2361	0.2296	RANDOM	41.39

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]
-5.5981	1.1333	0.2746	6.9256	-6.6996	-1.3275

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	2.76
t_omega_torsion	2.65
t_angle_deg	0.77
t_bond_d	0.006
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22937
Nucleic Acid Atoms
Solvent Atoms	1019
Heterogen Atoms	162

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing