7MQT

N-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300) with 5-deoxy substrate 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
2.97	58.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.437	α = 90
b = 173.454	β = 90
c = 44.04	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	CCD	ADSC QUANTUM 210r		2017-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95370	Australian Synchrotron	MX1

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	1.88	46.11	99.67	0.998	10.1	7.2		48503

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	1.88	1.95			0.702

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6VVA	1.88	46.11	48503	2470	99.659	0.156	0.1539	0.1967	21.308

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]
0.164			-0.539		0.375

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.375
r_dihedral_angle_4_deg	27.51
r_dihedral_angle_3_deg	11.76
r_dihedral_angle_1_deg	6.501
r_lrange_it	6.109
r_lrange_other	5.901
r_scangle_it	4.207
r_scangle_other	4.206
r_scbond_it	2.708
r_scbond_other	2.708
r_mcangle_other	2.363
r_mcangle_it	2.356
r_mcbond_it	1.647
r_mcbond_other	1.639
r_angle_refined_deg	1.632
r_angle_other_deg	1.455
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.213
r_xyhbond_nbd_refined	0.208
r_nbd_other	0.189
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.169
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.07
r_bond_refined_d	0.012
r_xyhbond_nbd_other	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3442
Nucleic Acid Atoms
Solvent Atoms	581
Heterogen Atoms	64

Software

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