2O55 | pdb_00002o55

Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (0.90 M lithium sulfate, 0.10 M sodium succinate pH 4), Cryoprotected with: well solution supplemented with up to 20% glycerol, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.427	α = 90
b = 102.427	β = 90
c = 51.709	γ = 120

Symmetry
Space Group	P 31 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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-11-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97923, 0.96400	APS	23-ID-D

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	2.8	36.387	97.4	0.099	15.064	12.7		7690

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	2.8	2.9	82.5		0.197	4.527	4.6	631

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	2.806	36.387	7678	352	97.412	0.195	0.192	0.21	0.255	0.26	RANDOM	17.983

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]
1.506	0.753		1.506		-2.258

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.546
r_dihedral_angle_3_deg	20.807
r_dihedral_angle_4_deg	19.714
r_dihedral_angle_1_deg	8.242
r_scangle_it	2.251
r_angle_refined_deg	1.486
r_scbond_it	1.363
r_mcangle_it	0.844
r_mcbond_it	0.46
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.546
r_dihedral_angle_3_deg	20.807
r_dihedral_angle_4_deg	19.714
r_dihedral_angle_1_deg	8.242
r_scangle_it	2.251
r_angle_refined_deg	1.486
r_scbond_it	1.363
r_mcangle_it	0.844
r_mcbond_it	0.46
r_nbtor_refined	0.316
r_nbd_refined	0.235
r_symmetry_vdw_refined	0.235
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2045
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.