7MFS | pdb_00007mfs

N-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300) with substrate and product bound

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
2.98	58.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.928	α = 90
b = 76.474	β = 90
c = 174.207	γ = 90

Symmetry
Space Group	P 2 21 21

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	ADSC QUANTUM 315r		2016-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95369	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	1.51	46.25	98.73	0.998	17.5	30.1		91961

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	1.51	1.56			0.661

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	1.51	46.25	91961	4620	98.725	0.181	0.1798	0.19	0.2099	0.22	12.515

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]
0.624			-0.207		-0.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.112
r_dihedral_angle_4_deg	31.125
r_dihedral_angle_3_deg	12.448
r_dihedral_angle_1_deg	6.5
r_lrange_it	6.185
r_lrange_other	6.131
r_scangle_it	2.877
r_scangle_other	2.876
r_mcangle_other	1.916
r_mcangle_it	1.915
r_scbond_it	1.85
r_scbond_other	1.849
r_angle_refined_deg	1.844
r_angle_other_deg	1.477
r_mcbond_it	1.206
r_mcbond_other	1.199
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.237
r_nbd_other	0.212
r_symmetry_nbd_other	0.195
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.166
r_chiral_restr	0.094
r_symmetry_xyhbond_nbd_other	0.087
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3440
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	80

Software

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