2Y4L

MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH Manganese and GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BO7	PDB ENTRY 2BO7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		4% V/V ETHYLENE GLYCOL, 0.1 M BIS-TRIS PROPANE PH 5.5, 0.2 MNCL2, 0.4 M SODIUM MALONATE.

Crystal Properties
Matthews coefficient	Solvent content
5.61	78.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.756	α = 90
b = 149.756	β = 90
c = 154.71	γ = 120

Symmetry
Space Group	P 32 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 CCD		2009-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	2.8	50	100	0.08	22.3	10.9		47314		2	54.9

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	2.8	2.9	100		0.59	3.9	10.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BO7	2.8	129.69	47314	2530	99.85	0.1893	0.18762	0.22041	RANDOM	48.073

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]
-0.49	-0.25		-0.49		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.28
r_dihedral_angle_3_deg	18.61
r_dihedral_angle_4_deg	16.612
r_dihedral_angle_1_deg	6.207
r_scangle_it	4.213
r_scbond_it	2.471
r_mcangle_it	1.676
r_angle_refined_deg	1.67
r_mcbond_it	0.837
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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	6179
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing