2HI0 | pdb_00002hi0

Crystal structure of putative phosphoglycolate phosphatase (YP_619066.1) from Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 at 1.51 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	277	0.2M NaOAc, 30.0% PEG-8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.636	α = 90
b = 38.695	β = 98.09
c = 103.583	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	2006-06-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97939	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.51	47.727	95.8	0.101	8.75	3.61		72271			19.143

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.51	1.56	82.6		0.537	2.1	2.77	5575

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	1.51	47.727	72257	3644	99.17	0.158	0.158	0.157	0.17	0.19	0.2	RANDOM	11.423

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]
-0.07		0.19	0.17		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.547
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	13.063
r_scangle_it	6.563
r_dihedral_angle_1_deg	5.487
r_scbond_it	4.43
r_mcangle_it	2.632
r_mcbond_it	1.707
r_angle_refined_deg	1.592
r_angle_other_deg	0.99
r_mcbond_other	0.532
r_symmetry_vdw_other	0.289
r_nbd_refined	0.229
r_metal_ion_refined	0.208
r_nbd_other	0.196
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.177
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.093
r_nbtor_other	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3675
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	81

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing