4KJX | pdb_00004kjx

Crystal Structure of the complex of three phase partition treated lipase from Thermomyces lanuginosa with Lauric acid and P-nitrobenzaldehyde (PNB) at 2.1 resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EA6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M HEPES, O.1M Nacl, 1.6M Ammonium sulphate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.997	α = 90
b = 139.997	β = 90
c = 80.492	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MARRESEARCH	Mirror	2012-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	2.1	50	98.6	0.086	35.3		98715	48911			40.5

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	2.1	2.14	98.6		0.443	2		48911

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	4EA6	2.1	45.83	98715	48888	2634	97.99	0.21679	0.21425	0.22	0.26528	0.27	RANDOM	35.951

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]
19.23			19.23		-38.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.064
r_dihedral_angle_4_deg	20.632
r_dihedral_angle_3_deg	16.965
r_dihedral_angle_1_deg	7.657
r_angle_refined_deg	2.068
r_angle_other_deg	1.108
r_chiral_restr	0.13
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.064
r_dihedral_angle_4_deg	20.632
r_dihedral_angle_3_deg	16.965
r_dihedral_angle_1_deg	7.657
r_angle_refined_deg	2.068
r_angle_other_deg	1.108
r_chiral_restr	0.13
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4140
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	111

Software

Software
Software Name	Purpose
CBASS	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.