8BRE

1,6-anhydro-n-actetylmuramic acid kinase (AnmK)

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	7.5	291	8% PEG 8000, 0.2M litium chloride, 0.05M magnesium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.67	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.093	α = 90
b = 90.093	β = 90
c = 178.378	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		2022-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979264	ALBA	XALOC

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	47.292	100	1	22.5	20.1		55214

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	2.05	100		1.688	0.667	2.1	20.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QBX	2	47.292	55167	2667	99.978	0.179	0.1776	0.2121	RANDOM	51.715

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]
-0.319			-0.319		0.638

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.426
r_dihedral_angle_6_deg	13.452
r_dihedral_angle_1_deg	6.299
r_lrange_it	5.524
r_lrange_other	5.487
r_dihedral_angle_2_deg	5.367
r_mcangle_it	3.525
r_mcangle_other	3.524
r_scangle_it	3.522
r_scangle_other	3.522
r_mcbond_it	2.437
r_mcbond_other	2.437
r_scbond_it	2.409
r_scbond_other	2.408
r_angle_refined_deg	1.04
r_angle_other_deg	0.473
r_nbd_refined	0.21
r_symmetry_nbd_other	0.189
r_nbd_other	0.187
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.141
r_symmetry_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.055
r_bond_other_d	0.009
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5413
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	2

Software

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