1YXY | pdb_00001yxy

Crystal Structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes (APC29713) Structural genomics, MCSG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	273	ammonium sulfate, BIS-TRIS buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.69	53.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.64	α = 90
b = 83.521	β = 90
c = 104.256	γ = 90

Symmetry
Space Group	P 21 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	SBC-3	horizontal-focussing Si-111 double-crystal monochromator and vertical-focusing mirror	2004-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979484	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	50	98.4	0.123	26	13	69461	68381	1	1	30.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	98.2		0.809	2.4	10.1	6793

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	SAD	THROUGHOUT	1.6	50	69461	65953	3508	99.53	0.19407	0.19337	0.19	0.20717	0.2	RANDOM	22.286

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			0.04		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.399
r_dihedral_angle_4_deg	13.491
r_dihedral_angle_3_deg	11.616
r_dihedral_angle_1_deg	4.769
r_scangle_it	2.54
r_scbond_it	1.734
r_angle_refined_deg	1.026
r_mcangle_it	0.787
r_mcbond_it	0.471
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.399
r_dihedral_angle_4_deg	13.491
r_dihedral_angle_3_deg	11.616
r_dihedral_angle_1_deg	4.769
r_scangle_it	2.54
r_scbond_it	1.734
r_angle_refined_deg	1.026
r_mcangle_it	0.787
r_mcbond_it	0.471
r_nbtor_refined	0.299
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.101
r_symmetry_hbond_refined	0.093
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3452
Nucleic Acid Atoms
Solvent Atoms	679
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.