3T2G | pdb_00003t2g

Fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus, Y229F variant with DHAP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T2B	PDB ENTRY 3T2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	8% PEG3350, 0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.43	α = 90
b = 112.43	β = 90
c = 151.52	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	PSI PILATUS 6M		2010-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.998	47.721	99.3	0.18	0.18	10.7	6.4	10089	10089	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.16	99.6		0.599	0.599	3	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 3T2B	3	47.72	2	9583	9573	505	100	0.1779	0.17487	0.17	0.23403	0.24	RANDOM	41.404

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]
1.45			1.45		-2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.051
r_dihedral_angle_3_deg	21.005
r_dihedral_angle_4_deg	20.13
r_dihedral_angle_1_deg	7.378
r_scangle_it	3.06
r_scbond_it	1.73
r_angle_refined_deg	1.6
r_mcangle_it	1.24
r_mcbond_it	0.642
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.051
r_dihedral_angle_3_deg	21.005
r_dihedral_angle_4_deg	20.13
r_dihedral_angle_1_deg	7.378
r_scangle_it	3.06
r_scbond_it	1.73
r_angle_refined_deg	1.6
r_mcangle_it	1.24
r_mcbond_it	0.642
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3005
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	22

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	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.