4S12

1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from Yersinia enterocolitica.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 7.6 mg/ml, 0.1 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME, Screen: JCSG+ (H7), 0.24M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.287	α = 90
b = 81.734	β = 103.21
c = 58.848	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 300 mm CCD	Beryllium lenses	2014-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.55	30	100	0.081	0.081	15.2	4.4		125532		-3	17.1

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)
1	1.55	1.58	100		0.505	0.505	2.8	4.4	6249

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4LZJ	1.55	29.95	119206	119206	6306	99.9	0.14467	0.14333	0.17002	RANDOM	20.071

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]
-0.9		-0.37	1.5		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.302
r_dihedral_angle_4_deg	13.985
r_dihedral_angle_3_deg	10.098
r_long_range_B_refined	6.215
r_long_range_B_other	5.937
r_dihedral_angle_1_deg	3.405
r_scangle_other	2.846
r_scbond_it	1.841
r_scbond_other	1.841
r_mcangle_it	1.647
r_mcangle_other	1.647
r_angle_refined_deg	1.478
r_mcbond_other	1.055
r_mcbond_it	1.054
r_angle_other_deg	0.785
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6404
Nucleic Acid Atoms
Solvent Atoms	979
Heterogen Atoms	52

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling