2HLH

Crystal structure of fucosyltransferase NodZ from Bradyrhizobium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	0.25M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.1	α = 90
b = 130.1	β = 90
c = 83.3	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 BW7A		EMBL/DESY, HAMBURG	BW7A

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	1.95	15	99.9	0.045	58.2	11.7		30716		-3	24.2

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	1.95	2.01	100		0.27	11.9	11.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2HHC	1.95	15	30716	30711	1085	99.9	0.162	0.161	0.206	RANDOM	27.03

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]
-0.13	-0.06		-0.13		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.644
r_dihedral_angle_4_deg	16.907
r_dihedral_angle_3_deg	12.597
r_dihedral_angle_1_deg	5.975
r_scangle_it	5.287
r_scbond_it	3.929
r_mcangle_it	1.704
r_angle_refined_deg	1.599
r_mcbond_it	1.339
r_symmetry_vdw_other	0.285
r_symmetry_vdw_refined	0.262
r_mcbond_other	0.255
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.198
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.091
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_nbd_other
r_nbtor_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	2301
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	20

Software

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