2P6P | pdb_00002p6p

X-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transferase UrdGT2

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	0.1M HEPES,18% PEG 1500, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.872	α = 90
b = 78.904	β = 90
c = 133.958	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	MARMOSAIC 225 mm CCD		2006-02-25	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2005-02-13	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.1036	SLS	X06SA
2	SYNCHROTRON	SLS BEAMLINE X06SA	1.0377, 1.0398, 0.8551	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.88	68.04	99.6	0.093	6.4	15.7	4.8	57551	57345			29.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.9	68	99.6		6.4	15.7	4.8	57346

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.88	68.04	54481	2868	99.65	0.19028	0.18823	0.189	0.22978	0.2305	RANDOM	30.096

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]
0.99			-0.21		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.651
r_dihedral_angle_4_deg	19.897
r_dihedral_angle_3_deg	17.664
r_dihedral_angle_1_deg	6.604
r_scangle_it	3.531
r_scbond_it	2.27
r_angle_refined_deg	1.584
r_mcangle_it	1.383
r_mcbond_it	0.904
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.253
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.12
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5734
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
SLS-X06SA	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	phasing