1YRR | pdb_00001yrr

Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		EXPERIMENTAL PHASES FROM AN IODINE SOAKED CRYSTAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4	293	sodium dihydrogenophosphate hydrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.00

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.157	α = 90
b = 114.554	β = 90
c = 80.208	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	IMAGE PLATE	MAR scanner 345 mm plate		1999-01-28	M	SINGLE WAVELENGTH
2	1	x-ray		M
3	1	x-ray		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1		LNLS	D03B-MX1

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
1,2,3	2	20	97.7	0.06	14.1	3.4		50702		2	35.8

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)
1,2,3	2	2.05	99.3		0.22	4.27	3.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	EXPERIMENTAL PHASES FROM AN IODINE SOAKED CRYSTAL	2	20	50702	48144	2540	97.7	0.161	0.159	0.2	0.199	0.23	RANDOM	17.92

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]
0.57			-0.96		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.751
r_scangle_it	4.607
r_scbond_it	2.837
r_angle_refined_deg	1.887
r_mcangle_it	1.845
r_angle_other_deg	1.593
r_mcbond_it	1.091
r_symmetry_vdw_other	0.32
r_symmetry_hbond_refined	0.308
r_symmetry_vdw_refined	0.272
r_nbd_other	0.249
r_nbd_refined	0.22
r_chiral_restr	0.202
r_xyhbond_nbd_refined	0.169
r_nbtor_other	0.091
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5371
Nucleic Acid Atoms
Solvent Atoms	435
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing