9H4X | pdb_00009h4x

Crystal structure of Ni2+ dependent glycerol-1-phosphate dehydrogenase AraM from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.2	293	20.0-25.5% (w/v) PEG 3350, 0.15-0.29 M KSCN

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.015	α = 90
b = 70.499	β = 95.51
c = 72.609	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 4M		2022-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	2.95	45.51	98.4	0.978	8	1.9		9676

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	2.95	3.13			0.433

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.95	43.036	9674	512	98.114	0.245	0.2406	0.2481	0.3102	0.3109	71.254

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]
-1.805		-0.435	-0.747		2.588

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.946
r_dihedral_angle_6_deg	15.495
r_dihedral_angle_2_deg	11.316
r_lrange_other	8.932
r_lrange_it	8.931
r_dihedral_angle_1_deg	6.267
r_scangle_it	5.21
r_scangle_other	5.209
r_mcangle_it	5.078
r_mcangle_other	5.077
r_scbond_it	3.185
r_scbond_other	3.184
r_mcbond_it	3.16
r_mcbond_other	3.16
r_angle_refined_deg	1.509
r_dihedral_angle_other_2_deg	1.312
r_angle_other_deg	0.517
r_nbd_other	0.255
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.187
r_symmetry_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.168
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.067
r_metal_ion_refined	0.03
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3027
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	55

Software

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