8AQF | pdb_00008aqf

CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND LEI-515

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MES pH 6.5, 6 to 13% PEG MME5K, 12% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.625	α = 90
b = 127.568	β = 90
c = 60.358	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS EIGER X 16M		2021-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00009	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.55	45.81	99.6	0.0631	0.9985	11.69	6.62		51415

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.65			0.7885	0.5966

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	3PE6	1.55	45.81	51370	2472	99.521	0.155	0.1544	0.17	0.1781	0.19	31.073

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]
2.711			-2.048		-0.663

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.594
r_dihedral_angle_4_deg	17.641
r_dihedral_angle_3_deg	14.443
r_lrange_it	6.965
r_lrange_other	6.687
r_dihedral_angle_1_deg	6.378
r_scangle_it	4.304
r_scangle_other	4.303
r_scbond_it	2.786
r_scbond_other	2.785
r_mcangle_other	2.638
r_mcangle_it	2.637
r_angle_refined_deg	2.019
r_mcbond_it	1.875
r_mcbond_other	1.872
r_angle_other_deg	1.53
r_symmetry_nbd_refined	0.359
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.176
r_nbd_other	0.169
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2238
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	34

Software

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