2PQ7 | pdb_00002pq7

Crystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	NANODROP, 24.0% 2-methyl-2,4-pentanediol, 0.2M Sodium chloride, 0.1M Sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.518	α = 90
b = 40.662	β = 95.32
c = 37.789	γ = 90

Symmetry
Space Group	C 1 2 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 mirror (vertical focusing)	2007-04-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97916, 0.97867	SSRL	BL11-1

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	1.45	27.441	99.9	0.065	0.065	7.2	3.7		37299			17.32

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)
	1.45	1.49	99.8		0.701	0.701	1.1	3.7	2695

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 (All)	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	1.45	27.441	37299	1864	99.85	0.183	0.183	0.183	0.19	0.193	0.2	RANDOM	20.351

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]
0.26		-0.96	-1.13		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.742
r_dihedral_angle_3_deg	12.714
r_dihedral_angle_4_deg	12.265
r_scangle_it	7.859
r_scbond_it	5.641
r_dihedral_angle_1_deg	3.536
r_mcangle_it	3.003
r_mcbond_it	2.218
r_angle_refined_deg	1.561
r_angle_other_deg	0.986
r_mcbond_other	0.524
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.218
r_symmetry_vdw_other	0.206
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.178
r_nbd_other	0.156
r_chiral_restr	0.103
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1444
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing