4K6A

Revised Crystal Structure of apo-form of Triosephosphate Isomerase (tpiA) from Escherichia coli at 1.8 Angstrom Resolution.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D11), 0.2M Calcium chloride, 0.1M Tris-HCl pH 8.0, 20% (w/v) PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.066	α = 90
b = 67.488	β = 90
c = 149.769	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	CCD	MARMOSAIC 300 mm CCD	Mirrors	2013-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.03326	APS	21-ID-D

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	1.8	30	99.9	0.088	18.3	5.8	44231	44231		-3	18.5

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	1.8	1.83	98.4		0.529	2.6	4.1	2158

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1TRE	1.8	29.06	41906	41906	2228	99.85	0.15075	0.15075	0.14895	0.1847	RANDOM	16.865

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]
0.02			-0.16		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.452
r_dihedral_angle_4_deg	10.237
r_dihedral_angle_3_deg	9.469
r_scangle_it	4.664
r_scbond_it	2.815
r_dihedral_angle_1_deg	2.769
r_mcangle_it	1.584
r_angle_refined_deg	1.327
r_mcbond_it	0.973
r_angle_other_deg	0.878

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.452
r_dihedral_angle_4_deg	10.237
r_dihedral_angle_3_deg	9.469
r_scangle_it	4.664
r_scbond_it	2.815
r_dihedral_angle_1_deg	2.769
r_mcangle_it	1.584
r_angle_refined_deg	1.327
r_mcbond_it	0.973
r_angle_other_deg	0.878
r_mcbond_other	0.329
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3786
Nucleic Acid Atoms
Solvent Atoms	546
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.