8CP9 | pdb_00008cp9

1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with non-hydrolyzable AMPPNP.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% PEG 3350, Na/K tartrate 0.2M

Crystal Properties
Matthews coefficient	Solvent content
2.62	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.94	α = 90
b = 89.94	β = 90
c = 176.958	γ = 120

Symmetry
Space Group	P 63

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 PILATUS 6M		2022-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	47.024	100	0.099	0.999	21	20.8		41089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	100		1.717	0.701	2.2	21.3

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	2.2	47.024	41048	2042	99.981	0.186	0.1833	0.22	0.231	0.27	53.71

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]
0.845			0.845		-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.519
r_dihedral_angle_6_deg	14.294
r_dihedral_angle_1_deg	7.277
r_lrange_it	6.944
r_lrange_other	6.932
r_dihedral_angle_2_deg	5.784
r_mcangle_it	4.822
r_mcangle_other	4.822
r_scangle_it	4.69
r_scangle_other	4.69
r_mcbond_it	3.387
r_mcbond_other	3.385
r_scbond_it	3.276
r_scbond_other	3.275
r_angle_refined_deg	1.159
r_angle_other_deg	0.64
r_nbd_other	0.236
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.221
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.166
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.058
r_metal_ion_refined	0.042
r_bond_other_d	0.015
r_symmetry_xyhbond_nbd_other	0.008
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5401
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	64

Software

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