7WOL | pdb_00007wol

Crystal structure of lipase TrLipB from Thermomocrobium roseum

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1M Succinic acid,0.1M HEPES,7,1% w/vPEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.402	α = 90
b = 129.402	β = 90
c = 122.792	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS PILATUS3 6M		2021-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	2	45.75	100	0.082	22.8	14.4		70819

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	2.04			0.821

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1lzk	2	45.75	70744	3497	99.983	0.159	0.1572	0.17	0.1862	0.2	39.58

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]
-1.717			-1.717		3.433

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.203
r_dihedral_angle_4_deg	19.61
r_dihedral_angle_3_deg	12.394
r_lrange_it	7.089
r_lrange_other	7
r_dihedral_angle_1_deg	6.212
r_scangle_it	5.397
r_scangle_other	5.396
r_mcangle_it	3.596
r_mcangle_other	3.596
r_scbond_it	3.562
r_scbond_other	3.561
r_mcbond_it	2.593
r_mcbond_other	2.592
r_angle_refined_deg	1.454
r_angle_other_deg	1.319
r_nbd_other	0.259
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.161
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.026
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4948
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	110

Software

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