2HRZ | pdb_00002hrz

The crystal structure of the nucleoside-diphosphate-sugar epimerase from Agrobacterium tumefaciens

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M Tris, 3.5M Na Formate, 0.1M MES6.0, 20% PEG10K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.893	α = 90
b = 112.893	β = 90
c = 52.765	γ = 120

Symmetry
Space Group	P 31 2 1

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 315	mirrors	2006-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9798	APS	19-ID

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	1.85	97.59	99.59	0.084	32.98	13.6	31621	31491	2	2	28

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	1.85	1.9	99.75		0.69	2.53	12.1	2313

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 (All)	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	1.85	37	31621	31491	1677	99.59	0.18647	0.18647	0.18455	0.1832	0.22457	0.2234	RANDOM	28.539

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]
0.52	0.26		0.52		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.357
r_dihedral_angle_4_deg	19.017
r_dihedral_angle_3_deg	13.624
r_dihedral_angle_1_deg	6.088
r_scangle_it	3.663
r_scbond_it	2.319
r_angle_refined_deg	1.243
r_mcangle_it	1.225
r_mcbond_it	0.862
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.357
r_dihedral_angle_4_deg	19.017
r_dihedral_angle_3_deg	13.624
r_dihedral_angle_1_deg	6.088
r_scangle_it	3.663
r_scbond_it	2.319
r_angle_refined_deg	1.243
r_mcangle_it	1.225
r_mcbond_it	0.862
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.2
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2621
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	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.