3D03 | pdb_00003d03

1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DXL	PDB ENTRY 2DXL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	277	60% Tacsimate, 100mM bis-tris, pH 7.0, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.967	α = 90
b = 133.842	β = 90
c = 168.941	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2007-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95367	Australian Synchrotron	MX1

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	1.9	43.3	96.7	0.098	11.9	4.2	163812	163812			16.2

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)
	1.9	2	91		0.613	1.9	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DXL	1.9	43.27	155501	8219	96.65	0.18623	0.18426	0.1869	0.22333	0.2236	RANDOM	8.215

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]
-0.14			0.05		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.18
r_dihedral_angle_4_deg	17.997
r_dihedral_angle_3_deg	15.381
r_dihedral_angle_1_deg	6.416
r_scangle_it	4.055
r_scbond_it	2.632
r_angle_refined_deg	1.557
r_mcangle_it	1.47
r_mcbond_it	0.905
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.229
r_symmetry_hbond_refined	0.225
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.124
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12858
Nucleic Acid Atoms
Solvent Atoms	1034
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing