2HX1 | pdb_00002hx1

Crystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.5	277	15.0% Ethanol, 0.2M MgCl2, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	47.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.624	α = 90
b = 119.462	β = 90
c = 151.274	γ = 90

Symmetry
Space Group	P 21 21 21

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	2006-06-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97932, 0.91837, 0.97915	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	2.1	29.323	100	0.152	0.152	4.4	3.7		70192			20.6

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)
	2.1	2.15	100		0.635	0.635	1.2	3.7	5087

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	2.1	29.323	70121	3531	99.92	0.181	0.18146	0.179	0.19	0.234	0.25	RANDOM	23.291

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]
-0.59			0.53		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.842
r_dihedral_angle_4_deg	15.681
r_dihedral_angle_3_deg	13.952
r_scangle_it	7.049
r_dihedral_angle_1_deg	6.433
r_scbond_it	5.194
r_mcangle_it	2.842
r_mcbond_it	1.837
r_angle_refined_deg	1.433
r_angle_other_deg	0.972
r_mcbond_other	0.383
r_symmetry_vdw_other	0.246
r_nbd_refined	0.209
r_nbd_other	0.187
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.179
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.161
r_nbtor_other	0.086
r_chiral_restr	0.082
r_metal_ion_refined	0.029
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8884
Nucleic Acid Atoms
Solvent Atoms	1035
Heterogen Atoms	138

Software

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