6NXS | pdb_00006nxs

Crystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C218Y mutant

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.2 M Calcium acetate hydrate 0.1M Sodium cacodylate trihydrate 6.5 18 % w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.38	α = 90
b = 97.211	β = 91.92
c = 68.148	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	CCD	MARMOSAIC 300 mm CCD		2017-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9786	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.52	68.2	99.1	0.076	0.086	0.039	0.996	9.7	4.6		93845

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.55	98.1		0.28	0.316	0.145	0.953		4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.52	68.2	88995	4834	99.11	0.1905	0.1895	0.2	0.2082	0.22	RANDOM	11.817

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]
1.56		-0.61	-0.51		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.334
r_dihedral_angle_4_deg	13.445
r_dihedral_angle_3_deg	10.305
r_dihedral_angle_1_deg	6.072
r_angle_refined_deg	1.808
r_angle_other_deg	1.506
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.334
r_dihedral_angle_4_deg	13.445
r_dihedral_angle_3_deg	10.305
r_dihedral_angle_1_deg	6.072
r_angle_refined_deg	1.808
r_angle_other_deg	1.506
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3699
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

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.