7MFN | pdb_00007mfn

N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphylococcus aureus (strain MRSA USA300)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VVA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1 M trisodium citrate, 0.1 M sodium cacodylate, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.999	α = 90
b = 174.446	β = 90
c = 44.523	γ = 90

Symmetry
Space Group	P 21 21 2

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 EIGER X 16M		2018-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95366	Australian Synchrotron	MX2

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	1.55	46.4	99.5	0.999	13.5	13.1		87948

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.57			0.842

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6VVA	1.55	42.004	87948	4414	99.449	0.152	0.1502	0.16	0.1779	0.19	19.856

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]
-0.244			0.147		0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.925
r_dihedral_angle_4_deg	29.585
r_dihedral_angle_3_deg	11.332
r_dihedral_angle_1_deg	6.282
r_lrange_it	6.166
r_lrange_other	6.166
r_scangle_it	4.307
r_scangle_other	4.306
r_scbond_it	2.813
r_scbond_other	2.812
r_mcangle_other	2.398
r_mcangle_it	2.395
r_angle_refined_deg	1.905
r_mcbond_it	1.716
r_mcbond_other	1.693
r_angle_other_deg	1.56
r_nbd_refined	0.244
r_nbd_other	0.242
r_symmetry_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.232
r_xyhbond_nbd_refined	0.21
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.168
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_symmetry_xyhbond_nbd_other	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3434
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	32

Software

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