6I8D | pdb_00006i8d

STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF BUTYL 4-NITROPHENYL HEXYLPHOSPHONATE

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JD4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	45 % PEG P400, 0.1 M BIS-TRIS pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.25	α = 90
b = 88.161	β = 90
c = 98.498	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	PIXEL	DECTRIS PILATUS3 S 6M	KB focusing mirrors	2018-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97924	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3.2	49.25	96.5	0.218	0.25	0.119	0.912	4.5	4.1		12184			43.084

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.42	96.2		0.525	0.609	0.298	0.675	2.2	3.9

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	5JD4	3.2	49.25	11539	622	95.31	0.22972	0.22733	0.23	0.27593	0.28	RANDOM	40.16

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]
2.85			-3.76		0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.232
r_dihedral_angle_4_deg	17.248
r_dihedral_angle_3_deg	13.342
r_dihedral_angle_1_deg	6.188
r_long_range_B_refined	6.139
r_long_range_B_other	6.139
r_scangle_other	3.195
r_mcangle_it	2.786
r_mcangle_other	2.786
r_scbond_it	1.857
r_scbond_other	1.857
r_mcbond_it	1.587
r_mcbond_other	1.583
r_angle_refined_deg	1.057
r_angle_other_deg	1.014
r_chiral_restr	0.061
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4771
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing