2BO7 | pdb_00002bo7

DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BO6	PDB ENTRY 2BO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				10 MM NACL, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 15% (V/V) MPD

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 406.699	α = 90
b = 162.14	β = 90
c = 108.431	γ = 90

Symmetry
Space Group	P 21 21 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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.95	40	90	0.1	13	4.3		151344		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	2.95	3.11	93		0.51	2.4	3.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BO6	2.95	223.61	140625	7443	97.8	0.208	0.207	0.21	0.224	0.22	RANDOM	63.38

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]
-0.21			0.71		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.299
r_dihedral_angle_3_deg	19.176
r_dihedral_angle_4_deg	18.077
r_dihedral_angle_1_deg	5.297
r_angle_refined_deg	1.439
r_scangle_it	1.042
r_scbond_it	0.76
r_symmetry_vdw_refined	0.468
r_symmetry_hbond_refined	0.437
r_mcangle_it	0.39
r_nbtor_refined	0.322
r_mcbond_it	0.289
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
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_vdw_other
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	31020
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	290

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL	data reduction
HKL	data scaling
MOLREP	phasing