3S5O

Crystal Structure of Human 4-hydroxy-2-oxoglutarate Aldolase Bound to Pyruvate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	PEG 3350, KSCN, Bis tris Propane, TCEP, Ethelyene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.75	74.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.23	α = 90
b = 141.23	β = 90
c = 108.388	γ = 120

Symmetry
Space Group	P 64 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	100	IMAGE PLATE	RIGAKU RAXIS IV		2009-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.97	35.17	99.9	0.05	20.8	13.82		45370

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	1.97	2.04	100		0.354	5.7	12.3	4465

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.97	34.648	2	45315	2287	99.69	0.1973	0.1963	0.2159	RANDOM	29.8862

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]
-0.52	-0.26		-0.52		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.151
r_dihedral_angle_4_deg	16.999
r_dihedral_angle_3_deg	14.222
r_dihedral_angle_1_deg	5.712
r_scangle_it	3.771
r_scbond_it	2.277
r_angle_refined_deg	1.429
r_mcangle_it	1.327
r_mcbond_it	0.707
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.151
r_dihedral_angle_4_deg	16.999
r_dihedral_angle_3_deg	14.222
r_dihedral_angle_1_deg	5.712
r_scangle_it	3.771
r_scbond_it	2.277
r_angle_refined_deg	1.429
r_mcangle_it	1.327
r_mcbond_it	0.707
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2246
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	25

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.