2XCU | pdb_00002xcu

Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, complex with CMP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5		HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND RESERVOIR (100 MM TRIS-HCL, PH 8.5, 35-40% (V/V) PEG 400, 200 MM NA-CITRATE, 50 MM 2-MERCAPTOETHANOL); SOAKING CRYSTALS IN 100 MM TRIS-HCL (PH 8.5), 36% (V/V) PEG 400, 200 MM NA-CITRATE AND 10 MM CMP FOR FOUR DAYS

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.77	α = 90
b = 44.67	β = 97.15
c = 143.64	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH SX-165		2009-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	2.42	31.85	97.2	0.04	21.3	3.6		62789		2	47.57

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	2.42	2.55	88.3		0.14	6.8	3

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 2XCI	2.42	31.22	59636	3139	97.22	0.20478	0.20236	0.2	0.25087	0.25	RANDOM	29.993

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]
-2.6		-0.3	6.95		-4.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.343
r_dihedral_angle_4_deg	19.815
r_dihedral_angle_3_deg	17.634
r_dihedral_angle_1_deg	6.555
r_scangle_it	3.501
r_scbond_it	2.027
r_angle_refined_deg	1.587
r_mcangle_it	1.407
r_mcbond_it	0.722
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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	11488
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	230

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing