3QBW | pdb_00003qbw

Crystal structure of pseudomonas aeruginosa 1,6-anhydro-n-actetylmuramic acid kinase (ANMK) bound to adenosine diphosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	296	25% PEG 4000, 0.2 M (NH4)2SO4, 0.1 M tri-Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.218	α = 90
b = 90.218	β = 90
c = 174.82	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	CCD	RAYONIX MX-300		2010-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.23	46.71	100	0.082	0.087	16.7	8.6	56308	39204		3	36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.23	2.35	99.8		0.397	0.43	4.6	6.8	5683

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	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	3CQY	2.23	46.71	39204	37465	1691	99.78	0.18884	0.18884	0.18783	0.21	0.21034	0.23	RANDOM	35.154

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]
-10.95			-10.95		21.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.586
r_dihedral_angle_4_deg	17.296
r_dihedral_angle_3_deg	14.164
r_dihedral_angle_1_deg	5.374
r_scangle_it	2.529
r_scbond_it	1.531
r_angle_refined_deg	1.173
r_mcangle_it	0.969
r_mcbond_it	0.514
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5228
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	64

Software

Software
Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling