8C0U | pdb_00008c0u

1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with their natural substrates and products

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	6	291	20% PEG 3350, Bis-Tris 0.1 M, pH 6.0, Li2SO4 0.2 M

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.583	α = 90
b = 90.583	β = 90
c = 174.478	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		2022-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979260	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.11	46.764	94.6	0.142	0.041	0.99	18.41	24.8		42080

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	2.11	2.19	64		0.785	0.518	1.555

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.112	46.764	42061	2057	90.69	0.232	0.2303	0.24	0.2681	0.27	RANDOM	48.191

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]
-0.136	-0.068		-0.136		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.715
r_dihedral_angle_6_deg	12.609
r_dihedral_angle_2_deg	7.25
r_dihedral_angle_1_deg	5.894
r_lrange_it	4.739
r_lrange_other	4.68
r_mcangle_it	2.941
r_mcangle_other	2.941
r_scangle_it	2.771
r_scangle_other	2.77
r_mcbond_it	1.79
r_mcbond_other	1.79
r_scbond_it	1.66
r_scbond_other	1.653
r_angle_refined_deg	0.849
r_dihedral_angle_other_2_deg	0.487
r_angle_other_deg	0.289
r_symmetry_nbd_other	0.199
r_nbd_refined	0.195
r_nbtor_refined	0.167
r_nbd_other	0.153
r_symmetry_nbd_refined	0.139
r_xyhbond_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.042
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	5502
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	97

Software

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