2PIM | pdb_00002pim

CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE, PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN (REUT_B4779) FROM RALSTONIA EUTROPHA JMP134 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	6.86	277	NANODROP, 1.32M Sodium citrate, 0.1M Sodium cacodylate pH 6.86, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.774	α = 90
b = 111.774	β = 90
c = 46.461	γ = 120

Symmetry
Space Group	P 6 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-04-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97934	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	28.748	100	0.141	0.141	4.7	14.1		9118

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	2.2	2.26	100		0.894	0.894	0.8	14.3	646

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 (All)	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	28.748	9116	514	100	0.185	0.185	0.182	0.19	0.222	0.22	RANDOM	28.728

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]
-2.32	-1.16		-2.32		3.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.336
r_dihedral_angle_3_deg	16.046
r_dihedral_angle_4_deg	12.453
r_scangle_it	7.143
r_dihedral_angle_1_deg	6.366
r_scbond_it	5.773
r_mcangle_it	2.99
r_mcbond_it	2.173
r_angle_refined_deg	1.604
r_angle_other_deg	0.803
r_mcbond_other	0.518
r_symmetry_vdw_other	0.281
r_symmetry_vdw_refined	0.229
r_xyhbond_nbd_refined	0.201
r_nbd_refined	0.194
r_nbd_other	0.186
r_nbtor_refined	0.167
r_symmetry_hbond_refined	0.165
r_chiral_restr	0.094
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	956
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing