3R12

Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.75 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	25.0% 1,2-propanediol, 10.0% Glycerol, 5.0% PEG-3000, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.812	α = 90
b = 51.818	β = 95.23
c = 84.735	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	ADSC QUANTUM 4	FLAT MIRROR	2002-03-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.918370,0.977757	SSRL	BL9-1

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	1.75	47.226	86.2	0.087	10.91	3.56		40637		-3	16.819

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	1.75	1.81	33.7		0.527	1.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.75	47.226	40622	2046	86.17	0.1548	0.1529	0.1915	RANDOM	22.0715

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]
-0.56		-0.56	-1.32		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.626
r_dihedral_angle_4_deg	15.687
r_dihedral_angle_3_deg	13.089
r_scangle_it	7.111
r_dihedral_angle_1_deg	6.137
r_scbond_it	4.878
r_mcangle_it	2.511
r_mcbond_it	1.573
r_angle_refined_deg	1.38
r_angle_other_deg	0.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.626
r_dihedral_angle_4_deg	15.687
r_dihedral_angle_3_deg	13.089
r_scangle_it	7.111
r_dihedral_angle_1_deg	6.137
r_scbond_it	4.878
r_mcangle_it	2.511
r_mcbond_it	1.573
r_angle_refined_deg	1.38
r_angle_other_deg	0.881
r_mcbond_other	0.473
r_chiral_restr	0.08
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3928
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	37

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

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 R01GM133198.