5A08 | pdb_00005a08

X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S4N	PDB ENTRY 1S4N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1M NA-CACODYLATE, PH 6.5 0.2M CAOAC 18% (W/V) PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.198	α = 90
b = 102.368	β = 90
c = 156.908	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PIXEL	KB MIRROR	2014-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.2	50	99.7	0.13	13.8	7.8		49674		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	2.2	2.28	97		0.65	3	8

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 1S4N	2.21	85.74	47109	2420	99.7	0.16502	0.16311	0.17	0.20273	0.21	RANDOM	24.972

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.921
r_dihedral_angle_4_deg	16.118
r_dihedral_angle_3_deg	13.707
r_dihedral_angle_1_deg	6.436
r_scangle_it	4.82
r_scbond_it	3.12
r_mcangle_it	3.082
r_mcbond_it	2.111
r_mcbond_other	2.111
r_angle_refined_deg	1.684
r_angle_other_deg	1.122
r_metal_ion_refined	0.461
r_symmetry_metal_ion_refined	0.446
r_symmetry_vdw_refined	0.393
r_nbd_refined	0.277
r_nbtor_refined	0.202
r_symmetry_vdw_other	0.196
r_nbd_other	0.195
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.102
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.08
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.006
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_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	6538
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing