3R13 | pdb_00003r13

Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	40.0% 1,2-propanediol, 0.05M calcium acetate, 0.1M acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.904	α = 90
b = 52.481	β = 95.59
c = 85.462	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 325 mm CCD	double crystal monochromator	2005-03-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.89194,0.97946,0.97929	SSRL	BL9-2

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	1.83	44.677	100	0.094	0.094	8.2	3.7		42195

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	1.83	1.93	100		0.552	0.552	2.4	3.7	6174

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	MAD	THROUGHOUT	1.83	44.677	42154	2116	99.97	0.1564	0.1545	0.16	0.1928	0.2	RANDOM	25.1014

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]
-0.8		-0.01	-0.38		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.897
r_dihedral_angle_4_deg	17.844
r_dihedral_angle_3_deg	13.512
r_scangle_it	8.161
r_dihedral_angle_1_deg	5.958
r_scbond_it	5.239
r_mcangle_it	2.822
r_mcbond_it	1.708
r_angle_refined_deg	1.432
r_angle_other_deg	0.899

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.897
r_dihedral_angle_4_deg	17.844
r_dihedral_angle_3_deg	13.512
r_scangle_it	8.161
r_dihedral_angle_1_deg	5.958
r_scbond_it	5.239
r_mcangle_it	2.822
r_mcbond_it	1.708
r_angle_refined_deg	1.432
r_angle_other_deg	0.899
r_mcbond_other	0.593
r_chiral_restr	0.091
r_bond_refined_d	0.016
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	3978
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
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 R01GM157729.