9SQJ | pdb_00009sqj

Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes with bound AMPPNP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9SQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	17% (w/v) PEG 3350 0.2 M HEPES pH 7.0 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.289	α = 90
b = 101.21	β = 90
c = 177.296	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2023-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03321	PETRA III, DESY	P11

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	1.981	49.112	99.55	0.1669	0.1756	0.05389	0.998	11.12	10.3		110500

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	1.981	2.051	99.14		0.703	0.474	1.05	10.1

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	1.981	49.112	110497	1547	99.559	0.181	0.1803	0.1896	0.2173	0.2358	49.396

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]
-1.497			1.3		0.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.995
r_dihedral_angle_4_deg	20.896
r_dihedral_angle_3_deg	13.829
r_lrange_it	8.157
r_lrange_other	8.156
r_dihedral_angle_1_deg	7.118
r_scangle_it	6.808
r_scangle_other	6.808
r_scbond_it	4.942
r_scbond_other	4.941
r_mcangle_other	4.848
r_mcangle_it	4.847
r_mcbond_it	3.672
r_mcbond_other	3.67
r_angle_other_deg	2.386
r_angle_refined_deg	1.593
r_chiral_restr_other	0.452
r_nbd_other	0.355
r_symmetry_nbd_refined	0.272
r_symmetry_nbd_other	0.216
r_symmetry_xyhbond_nbd_refined	0.211
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.167
r_xyhbond_nbd_other	0.133
r_chiral_restr	0.073
r_symmetry_nbtor_other	0.071
r_symmetry_xyhbond_nbd_other	0.069
r_bond_other_d	0.036
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10153
Nucleic Acid Atoms
Solvent Atoms	719
Heterogen Atoms	78

Software

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