8ZOZ | pdb_00008zoz

Crystal structure of the complex of glyceraldehyde-3-phosphate dehydrogenase of type B from Acinetobacter baumannii with Adenosine monophosphate at 3.20 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	298	0.2M MgSo4. 6H2O, 0.1M HEPES sodium (pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.509	α = 90
b = 167.732	β = 90
c = 150.726	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS EIGER2 X 9M		2023-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	3.2	89.26	97.2	0.23	0.24	0.069	0.998	7.9	12.8		30330

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.37	99.7		2.39	2.51	0.757	0.86	1.1	10.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.2	84.007	30303	1202	97.181	0.204	0.2012	0.21	0.2793	0.27	129.269

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]
12.992			-18.822		5.831

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.651
r_lrange_other	15.651
r_dihedral_angle_3_deg	14.152
r_dihedral_angle_6_deg	12.489
r_scangle_it	11.558
r_scangle_other	11.557
r_mcangle_it	11.256
r_mcangle_other	11.256
r_dihedral_angle_1_deg	7.284
r_mcbond_it	7.172
r_mcbond_other	7.172
r_scbond_it	7.01
r_scbond_other	7.007
r_dihedral_angle_2_deg	5.483
r_angle_refined_deg	1.112
r_dihedral_angle_other_2_deg	0.853
r_angle_other_deg	0.402
r_nbd_other	0.224
r_nbd_refined	0.212
r_symmetry_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.148
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.05
r_symmetry_xyhbond_nbd_other	0.027
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10716
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building