2HDO | pdb_00002hdo

Crystal structure of putative phosphoglycolate phosphatase (np_784602.1) from Lactobacillus plantarum at 1.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	4.2	277	0.4M KH2PO3, 1.6M NaH2PO3, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2	43.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.89	α = 90
b = 86.89	β = 90
c = 47.19	γ = 120

Symmetry
Space Group	P 61

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	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2006-05-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979224, 0.978954, 0.918370	SSRL	BL11-1

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	1.5	29.424	96.5	0.143	7.33	8.784		32658			22.126

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	1.5	1.55	88.8		0.426	2.32		4246

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.5	29.424	30840	1564	95.21	0.178	0.176	0.19	0.209	0.21	RANDOM	15.763

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]
-0.65	-0.33		-0.65		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.027
r_dihedral_angle_4_deg	14.608
r_dihedral_angle_3_deg	12.157
r_scangle_it	6.504
r_dihedral_angle_1_deg	5.575
r_scbond_it	4.578
r_mcangle_it	2.765
r_mcbond_it	1.984
r_angle_refined_deg	1.478
r_angle_other_deg	0.808
r_mcbond_other	0.486
r_nbd_refined	0.229
r_nbtor_refined	0.183
r_nbd_other	0.173
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.144
r_symmetry_vdw_other	0.12
r_symmetry_vdw_refined	0.088
r_nbtor_other	0.086
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1574
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	10

Software

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