2Q14 | pdb_00002q14

Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	NANODROP, 15.0% PEG 8000, 8.0% Ethylene glycol, 0.1M Bicine pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.436	α = 90
b = 137.504	β = 90
c = 279.051	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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-08-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97925, 0.97939, 0.94926	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	2.2	49.029	98.3	0.164	5.73			224828		-3	34.1

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	2.2	2.43	89.3		0.806	1.6

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	2.2	49.029	221971	11153	98.75	0.21	0.207	0.2122	0.252	0.2539	RANDOM	26.737

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]
1.32			-1.03		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.566
r_dihedral_angle_4_deg	18.2
r_dihedral_angle_3_deg	15.206
r_scangle_it	6.276
r_dihedral_angle_1_deg	5.647
r_scbond_it	4.784
r_mcangle_it	2.673
r_mcbond_it	1.686
r_angle_refined_deg	1.416
r_angle_other_deg	0.958
r_mcbond_other	0.383
r_nbd_refined	0.219
r_nbd_other	0.196
r_symmetry_vdw_other	0.193
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.181
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_refined	0.142
r_nbtor_other	0.088
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.07
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25568
Nucleic Acid Atoms
Solvent Atoms	1624
Heterogen Atoms	261

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing