3T2D | pdb_00003t2d

Fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus, FBP-bound form

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
2.62	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.291	α = 90
b = 112.291	β = 90
c = 151.348	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	1	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	1.36	54.78	99.9	0.073	0.073	18.5	9.2	103107	102981	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	1.36	1.39	99.9		0.424	0.424	5.1	8.5

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	1.36	54.78	2	97834	97834	5147	99.87	0.10475	0.10364	0.1	0.1259	0.12	RANDOM

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]
0.08			0.08		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.014
r_dihedral_angle_4_deg	17.468
r_dihedral_angle_3_deg	14.154
r_scangle_it	8.104
r_dihedral_angle_1_deg	6.644
r_scbond_it	5.677
r_mcangle_it	3.695
r_mcbond_it	2.56
r_rigid_bond_restr	2.512
r_angle_refined_deg	2.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.014
r_dihedral_angle_4_deg	17.468
r_dihedral_angle_3_deg	14.154
r_scangle_it	8.104
r_dihedral_angle_1_deg	6.644
r_scbond_it	5.677
r_mcangle_it	3.695
r_mcbond_it	2.56
r_rigid_bond_restr	2.512
r_angle_refined_deg	2.365
r_angle_other_deg	1.178
r_mcbond_other	0.908
r_chiral_restr	0.159
r_bond_refined_d	0.031
r_gen_planes_refined	0.013
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3057
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	24

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.