5IE7 | pdb_00005ie7

Crystal structure of a lactonase double mutant in complex with substrate b

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WZL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	24% PEG 2000 MME, 0.1M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.408	α = 90
b = 86.408	β = 90
c = 470.449	γ = 120

Symmetry
Space Group	P 61 2 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		2015-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	1.0	NSRRC	BL13C1

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	2.5	25	99.8	0.065	0.076	0.038	9.3	3.8		37570

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	2.5	2.59	99.5		0.357		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	3WZL	2.5	25	35550	1870	99.62	0.22078	0.21719	0.24	0.2891	0.31	RANDOM	36.141

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]
0.62	0.31		0.62		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.113
r_dihedral_angle_3_deg	20.193
r_dihedral_angle_4_deg	13.833
r_dihedral_angle_1_deg	8.877
r_long_range_B_refined	8.501
r_long_range_B_other	8.5
r_scangle_other	5.857
r_mcangle_it	5.275
r_mcangle_other	5.274
r_scbond_it	3.867
r_scbond_other	3.865
r_mcbond_other	3.501
r_mcbond_it	3.5
r_angle_refined_deg	1.513
r_angle_other_deg	1.002
r_chiral_restr	0.112
r_gen_planes_refined	0.017
r_bond_refined_d	0.01
r_gen_planes_other	0.008
r_bond_other_d	0.003
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	5034
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	46

Software

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