3MZ2 | pdb_00003mz2

Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	27.0000% polyethylene glycol 4000, 0.3000M ammonium sulfate, 0.1M sodium acetate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.577	α = 90
b = 90.481	β = 111.95
c = 60.373	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 mirror (vertical focusing)	2009-12-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97925,0.97895	SSRL	BL11-1

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	1.55	47.615	100	0.08	8.7	3.8		77355			14.681

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)
	1.55	1.63	100		0.61	0.61	2.3	3.7	11285

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	1.55	47.615	77315	3882	99.98	0.167	0.166	0.18	0.197	0.21	RANDOM	19.3

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]
0.15		-0.34	-0.95		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.904
r_dihedral_angle_4_deg	14.262
r_dihedral_angle_3_deg	13.113
r_dihedral_angle_1_deg	6.129
r_scangle_it	4.029
r_scbond_it	2.535
r_angle_refined_deg	1.592
r_mcangle_it	1.402
r_angle_other_deg	0.938
r_mcbond_it	0.824

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.904
r_dihedral_angle_4_deg	14.262
r_dihedral_angle_3_deg	13.113
r_dihedral_angle_1_deg	6.129
r_scangle_it	4.029
r_scbond_it	2.535
r_angle_refined_deg	1.592
r_mcangle_it	1.402
r_angle_other_deg	0.938
r_mcbond_it	0.824
r_mcbond_other	0.283
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4532
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing
SOLVE	phasing

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.