3O0D

Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	285	30% MPD, 0.1M MES, 0.02M CaCl2, 0.2M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.354	α = 90
b = 132.141	β = 90
c = 137.255	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	CCD	ADSC QUANTUM 315r		2007-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9395	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.7	20	99.5	0.073	6.7	4.1	229642	228540			18.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.79	99.9		0.343	2.2	4.2	33221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	20	229642	216938	11428	99.5	0.17264	0.17264	0.17062	0.21096	RANDOM	22.943

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]
-0.59			0.73		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.623
r_dihedral_angle_4_deg	17.206
r_dihedral_angle_3_deg	14.74
r_dihedral_angle_1_deg	6.668
r_scangle_it	4.824
r_scbond_it	3.221
r_mcangle_it	2.244
r_angle_refined_deg	2.109
r_mcbond_it	1.411
r_chiral_restr	0.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.623
r_dihedral_angle_4_deg	17.206
r_dihedral_angle_3_deg	14.74
r_dihedral_angle_1_deg	6.668
r_scangle_it	4.824
r_scbond_it	3.221
r_mcangle_it	2.244
r_angle_refined_deg	2.109
r_mcbond_it	1.411
r_chiral_restr	0.169
r_bond_refined_d	0.027
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16269
Nucleic Acid Atoms
Solvent Atoms	1653
Heterogen Atoms	339

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.