2CJP | pdb_00002cjp

Structure of potato (Solanum tuberosum) epoxide hydrolase I (StEH1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VJ5	PDB ENTRY 1VJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% PEG 10, 000), AND EQUILIBRATED BY SITTING-DROP VAPOR DIFFUSION AT ROOM TEMPERATURE.

Crystal Properties
Matthews coefficient	Solvent content
2.2	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.926	α = 90
b = 98.532	β = 90
c = 122.033	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	ADSC CCD		2004-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.95	31.6	99.2	0.06	20.9	5.1		49514			30.41

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	1.95	2.06	98.6		0.47	3.1	5

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 1VJ5	1.95	31.6	47002	2510	99	0.205	0.203	0.2	0.24	0.24	RANDOM	32.8

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]
-1.26			2.73		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.025
r_dihedral_angle_4_deg	17.744
r_dihedral_angle_3_deg	12.822
r_dihedral_angle_1_deg	5.248
r_scangle_it	1.512
r_angle_refined_deg	1.064
r_scbond_it	0.957
r_mcangle_it	0.823
r_mcbond_it	0.475
r_nbtor_refined	0.303
r_nbd_refined	0.179
r_symmetry_vdw_refined	0.144
r_symmetry_hbond_refined	0.136
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5115
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing