3I6Y | pdb_00003i6y

Structure of an esterase from the oil-degrading bacterium Oleispira antarctica

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PV1	PDB entry 1PV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	294	0.2 M diammonium hydrogen citrate, 20% PEG 3350, Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.845	α = 90
b = 88.179	β = 94.75
c = 84.104	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	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2009-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54178

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	1.7	27.94	86.9	0.103	16.338	3.8	71147	61811		-3	15.8

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	1.7	1.76	64.8		0.313	5.8	3.3	4596

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	PHASER	THROUGHOUT	PDB entry 1PV1	1.75	27.94	57845	3072	92.42	0.19053	0.18848	0.19	0.22898	0.23	RANDOM	15.966

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]
-0.01		0.03	0.09		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.599
r_dihedral_angle_4_deg	14.39
r_dihedral_angle_3_deg	14.165
r_dihedral_angle_1_deg	6.761
r_scangle_it	3.43
r_scbond_it	2.394
r_angle_refined_deg	1.484
r_mcangle_it	1.281
r_mcbond_it	0.891
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4358
Nucleic Acid Atoms
Solvent Atoms	508
Heterogen Atoms	33

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling