3DCI | pdb_00003dci

The Structure of a putative arylesterase from Agrobacterium tumefaciens str. C58

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.1M sodium acetate pH 4.6, 3.2M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.204	α = 90
b = 131.397	β = 90
c = 122.332	γ = 90

Symmetry
Space Group	C 2 2 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	CUSTOM-MADE		2006-11-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97921, 0.97941	APS	19-BM

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	50	99.7	0.088	6.5	7.4	41107	41107		-3	26.9

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	2.05	99.6		0.452		6.9	2712

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	34.28	39487	39487	1986	99.6	0.149	0.149	0.148	0.1558	0.184	0.1888	RANDOM	22.009

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]
0.7			0.3		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.158
r_dihedral_angle_4_deg	17.183
r_dihedral_angle_3_deg	12.591
r_dihedral_angle_1_deg	5.322
r_scangle_it	3.439
r_scbond_it	2.409
r_angle_refined_deg	1.386
r_mcangle_it	1.201
r_mcbond_it	1.057
r_angle_other_deg	0.967
r_symmetry_vdw_refined	0.296
r_symmetry_vdw_other	0.246
r_nbd_refined	0.211
r_nbd_other	0.196
r_symmetry_hbond_refined	0.194
r_mcbond_other	0.192
r_metal_ion_refined	0.184
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.137
r_nbtor_other	0.085
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4593
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	35

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building