3HJE | pdb_00003hje

Crystal structure of sulfolobus tokodaii hypothetical maltooligosyl trehalose synthase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IV8	PDB ENTRY 1IV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.89	293	0.2M Potassium sodium tartrate tetrahydrate, 20%(w/v) PEG3350, pH 5.89, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.992	α = 90
b = 86.1	β = 95.43
c = 70.13	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	IMAGE PLATE	RIGAKU RAXIS VII		2007-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	69.843	99.6				59664

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	99.9

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 (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 1IV8	1.9	19.94	59664	56580	3014		0.17245	0.17065	0.17	0.20606	0.21	RANDOM	23.399

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.613
r_dihedral_angle_4_deg	15.528
r_dihedral_angle_3_deg	12.702
r_dihedral_angle_1_deg	5.596
r_scangle_it	2.157
r_scbond_it	1.413
r_angle_refined_deg	1.079
r_mcangle_it	0.9
r_mcbond_it	0.542
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.613
r_dihedral_angle_4_deg	15.528
r_dihedral_angle_3_deg	12.702
r_dihedral_angle_1_deg	5.596
r_scangle_it	2.157
r_scbond_it	1.413
r_angle_refined_deg	1.079
r_mcangle_it	0.9
r_mcbond_it	0.542
r_nbtor_refined	0.301
r_nbd_refined	0.182
r_symmetry_vdw_refined	0.165
r_xyhbond_nbd_refined	0.112
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5902
Nucleic Acid Atoms
Solvent Atoms	858
Heterogen Atoms	24

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.