1O1Z

Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9.6	277	40% (v/v) PEG-600, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 9.60

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.41	α = 90
b = 41.79	β = 90
c = 51.72	γ = 90

Symmetry
Space Group	P 21 21 2

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	APS-1	water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2002-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.98011, 0.97938, 0.97918, 0.95671	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	50	100	0.05	62.01	6.71		38012

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	95.3		0.196	10.06	3.51

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	1.6	48.18	36027	1926	97.8	0.141	0.139	0.18	RANDOM	13.32

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]
			0.06		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.05
r_dihedral_angle_4_deg	19.046
r_dihedral_angle_3_deg	10.828
r_scangle_it	6.905
r_dihedral_angle_1_deg	6.079
r_scbond_it	4.411
r_mcangle_it	3.054
r_mcbond_it	1.79
r_angle_refined_deg	1.411
r_angle_other_deg	0.882
r_symmetry_vdw_other	0.336
r_symmetry_vdw_refined	0.306
r_symmetry_hbond_refined	0.244
r_nbd_other	0.238
r_xyhbond_nbd_refined	0.23
r_nbd_refined	0.211
r_metal_ion_refined	0.115
r_chiral_restr	0.091
r_nbtor_other	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1831
Nucleic Acid Atoms
Solvent Atoms	422
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	model building
SOLVE	phasing
ARP/wARP	model building
REFMAC	refinement
RESOLVE	phasing