5Z97

Crystal structure of a lactonase double mutant in complex with ligand N

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IE4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.2M Ammonium Sulfate, 0.085M Sodium Cacodylate pH 6.5, 25-28%(w/v) Polyethylene Glycol 8000, 15%(v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.319	α = 90
b = 110.52	β = 99.93
c = 127.779	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	CCD	RAYONIX MX-300		2017-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.32	25	95	0.067	0.077	0.038	12.6	3.9		50048

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	2.32	2.4	96.6		0.486	0.561	0.276	0.803		3.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5IE4	2.32	25	47531	2490	94.86	0.21236	0.20958	0.26634	RANDOM	48.23

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]
-1.8		0.53	0.12		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.469
r_dihedral_angle_3_deg	21.143
r_dihedral_angle_4_deg	18.072
r_long_range_B_refined	10.616
r_long_range_B_other	10.615
r_mcangle_it	7.25
r_mcangle_other	7.25
r_scangle_other	7.086
r_dihedral_angle_1_deg	5.815
r_mcbond_it	5.254
r_mcbond_other	5.251
r_scbond_it	5.22
r_scbond_other	5.219
r_angle_refined_deg	1.196
r_angle_other_deg	0.725
r_chiral_restr	0.077
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_gen_planes_other	0.003
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	8174
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing