6OR3 | pdb_00006or3

Structure of an Acyl Intermediate of Thermomyces Lanuginosa Lipase With Palmitic Acid in an Orthorhombic Crystal

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	Using filtered culture media with active fungal cells as the stock protein solution, about 30 mg/ml. Sitting drop equal amounts of the protein stock and the reservoir which was 20% PEG 335 buffered with 0.10 M MES at pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.17	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.865	α = 90
b = 85.268	β = 90
c = 86.741	γ = 90

Symmetry
Space Group	I 2 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	173	PIXEL	DECTRIS PILATUS 300K		2019-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1158	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim 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	1.45	60.8	99.9	0.334	0.32	0.337	0.997	10.4	62.8		46198			23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47	97.8		3.6	3.7	0.294	0.6	38.7

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	1TIB	1.45	60	43893	2291	99.94	0.16355	0.16111	0.17	0.21143	0.21	RANDOM	35.572

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]
3.1			1.92		-5.02

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	54.524
r_dihedral_angle_2_deg	34.281
r_sphericity_bonded	25.706
r_dihedral_angle_4_deg	19.379
r_dihedral_angle_3_deg	13.371
r_scangle_other	7.599
r_scbond_other	7.168
r_scbond_it	7.167
r_long_range_B_refined	7.039
r_long_range_B_other	7.038
r_rigid_bond_restr	6.703
r_dihedral_angle_1_deg	6.31
r_mcangle_other	5.701
r_mcangle_it	5.7
r_mcbond_it	5.044
r_mcbond_other	5.031
r_angle_refined_deg	1.688
r_angle_other_deg	1.501
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2071
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	32

Software

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