4GLB | pdb_00004glb

Structure of p-nitrobenzaldehyde inhibited lipase from Thermomyces lanuginosa at 2.69 A 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
3.87	68.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.911	α = 90
b = 139.911	β = 90
c = 80.448	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	2012-05-26	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	2.69	50	99	0.074	23			23546			48.1

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	2.69	2.74	90		0.273	3.7		48050

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-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	2.69	50	23546	1286	99	0.1635	0.1635	0.1613	0.15	0.20543	0.19	RANDOM	36.973

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]
18.29			18.29		-36.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.54
r_dihedral_angle_4_deg	21.478
r_dihedral_angle_3_deg	16.232
r_dihedral_angle_1_deg	5.856
r_scangle_it	1.428
r_angle_refined_deg	1.078
r_scbond_it	0.84
r_mcangle_it	0.821
r_mcbond_it	0.444
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.54
r_dihedral_angle_4_deg	21.478
r_dihedral_angle_3_deg	16.232
r_dihedral_angle_1_deg	5.856
r_scangle_it	1.428
r_angle_refined_deg	1.078
r_scbond_it	0.84
r_mcangle_it	0.821
r_mcbond_it	0.444
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4142
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	34

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.