2X4G | pdb_00002x4g

Crystal structure of PA4631, a nucleoside-diphosphate-sugar epimerase from Pseudomonas aeruginosa

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		2.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. CRYSTAL WAS SOAKED IN 20MM TRIMETHYLLEADCHLORIDE FOR APPROXIMATELY 5 MINUTES BEFORE BEING BACK SOAKED IN CRYO BUFFER

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.38	α = 90
b = 83.38	β = 90
c = 215.72	γ = 120

Symmetry
Space Group	P 62 2 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 CCD	MIRRORS	2008-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.65	41.7	97	0.08	23.3	5		12600

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	2.65	2.7	90		0.66	2.75	3.4

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 (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	NONE	2.65	41.7	12600	679	97	0.21346	0.21142	0.21	0.25314	0.25	RANDOM	30.888

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]
0.92	0.46		0.92		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.401
r_dihedral_angle_4_deg	18.631
r_dihedral_angle_3_deg	16.635
r_dihedral_angle_1_deg	6.319
r_scangle_it	2.945
r_scbond_it	1.691
r_angle_refined_deg	1.332
r_mcangle_it	1.111
r_angle_other_deg	0.845
r_mcbond_it	0.564
r_mcbond_other	0.078
r_chiral_restr	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2301
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
SHELXCDE	phasing