2HHC

Crystal structure of fucosyltransferase NodZ from Bradyrhizobium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	0.25M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.2	α = 90
b = 124.2	β = 90
c = 96.1	γ = 120

Symmetry
Space Group	P 65 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	MAR CCD 165 mm		2004-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8128	EMBL/DESY, HAMBURG	X11

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	1.54	15	100	0.05	72.5	24.4		64545		-3	26.31

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	1.54	1.57	100		0.802	3.8	17.8	3171

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.54	15	62474	62469	1270	96.8	0.183	0.182	0.197	RANDOM	29.03

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]
-1.04	-0.52		-1.04		1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.293
r_dihedral_angle_4_deg	20.705
r_dihedral_angle_3_deg	12.95
r_dihedral_angle_1_deg	5.523
r_scangle_it	3.786
r_scbond_it	2.672
r_angle_refined_deg	1.705
r_mcangle_it	1.508
r_mcbond_it	1.284
r_mcbond_other	0.321
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.215
r_nbd_other	0.205
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.186
r_symmetry_vdw_other	0.16
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.1
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2341
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	23

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing