3HC1

Crystal structure of HDOD domain protein with unknown function (NP_953345.1) from GEOBACTER SULFURREDUCENS at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.2000M KThioCyanate, 20.0000% PEG-3350, No Buffer pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.567	α = 90
b = 66.631	β = 111.96
c = 54.412	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	Flat collimating mirror, toroid focusing mirror	2009-03-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97932,0.97911	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	1.9	28.375	100	0.09	0.09	11.6	3.8		24939			23.082

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	1.9	1.95	100		0.761	0.761	1.9	3.8	1820

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	1.9	28.375	24920	1268	99.96	0.182	0.18	0.226	RANDOM	26.721

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]
-1.49		0.71	1.04		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.629
r_dihedral_angle_4_deg	15.443
r_dihedral_angle_3_deg	14.375
r_scangle_it	7.655
r_scbond_it	5.441
r_dihedral_angle_1_deg	5.217
r_mcangle_it	3.179
r_mcbond_it	2.054
r_angle_refined_deg	1.574
r_angle_other_deg	1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.629
r_dihedral_angle_4_deg	15.443
r_dihedral_angle_3_deg	14.375
r_scangle_it	7.655
r_scbond_it	5.441
r_dihedral_angle_1_deg	5.217
r_mcangle_it	3.179
r_mcbond_it	2.054
r_angle_refined_deg	1.574
r_angle_other_deg	1.06
r_mcbond_other	0.595
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2312
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing

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.