2PW9

Crystal structure of a putative formate dehydrogenase accessory protein from Desulfotalea psychrophila

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	100 mM Sodium MES pH 6.5, 22% PEG 8000, 200 mM Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.987	α = 90
b = 99.257	β = 109.7
c = 88.502	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	MAR CCD 165 mm		2007-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2.1	25.375	98.2	0.108	0.108	12.4	3.8	57870	57870			25.6

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	2.1	2.21	97.4		0.434	0.434	2.6	3.6	8392

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.1	20	57805	57805	2937	98.24	0.199	0.196	0.259	RANDOM	35.581

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]
-2.39		-0.04	3.04		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.588
r_dihedral_angle_4_deg	22.278
r_dihedral_angle_3_deg	18.589
r_dihedral_angle_1_deg	6.772
r_scangle_it	4.419
r_scbond_it	2.804
r_mcangle_it	1.679
r_angle_refined_deg	1.651
r_mcbond_it	1.045
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.588
r_dihedral_angle_4_deg	22.278
r_dihedral_angle_3_deg	18.589
r_dihedral_angle_1_deg	6.772
r_scangle_it	4.419
r_scbond_it	2.804
r_mcangle_it	1.679
r_angle_refined_deg	1.651
r_mcbond_it	1.045
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.115
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7064
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.