4B9E | pdb_00004b9e

Structure of a putative epoxide hydrolase from Pseudomonas aeruginosa, with bound MFA.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y37	PDB ENTRY 1Y37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.1 M LI2SO4, 1.25 M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.92	α = 90
b = 83.92	β = 90
c = 140.95	γ = 90

Symmetry
Space Group	P 41 21 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	ADSC QUANTUM 315r		2012-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.4	36.83	99.7	0.09	11.5	6.2		99408		2	13.7

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	1.4	1.48	99.3		0.69	2.4	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 1Y37	1.4	36.27	94130	4952	99.68	0.11165	0.1104	0.13	0.13525	0.15	RANDOM	17.522

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.614
r_dihedral_angle_2_deg	30.306
r_dihedral_angle_4_deg	19.155
r_sphericity_bonded	12.522
r_dihedral_angle_3_deg	12.136
r_mcbond_other	11.304
r_mcbond_it	10.937
r_dihedral_angle_1_deg	5.334
r_rigid_bond_restr	3.69
r_angle_refined_deg	1.72
r_angle_other_deg	0.912
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.279
r_nbd_other	0.221
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.188
r_symmetry_vdw_other	0.179
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.113
r_nbtor_other	0.107
r_xyhbond_nbd_other	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2346
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	57

Software

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