7Q2O | pdb_00007q2o

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#1)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	2.20 M (NH4)2SO4, 0.5 M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.667	α = 90
b = 70.145	β = 90
c = 179.018	γ = 90

Symmetry
Space Group	I 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	PIXEL	DECTRIS PILATUS 2M		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91840	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	45.45	99.2	0.074	0.999	14.42	5.52		32842

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.91			1.191	0.851

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	1BSY	1.8	45.45	32839	1000	99.229	0.184	0.1829	0.19	0.2206	0.23	44.116

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]
-2.279			4.523		-2.244

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.381
r_lrange_other	18.511
r_lrange_it	18.452
r_scangle_it	17.498
r_scangle_other	17.494
r_scbond_it	15.684
r_scbond_other	15.678
r_dihedral_angle_3_deg	13.803
r_dihedral_angle_4_deg	9.852
r_mcangle_other	9.73
r_mcangle_it	9.729
r_mcbond_it	9.255
r_mcbond_other	9.244
r_dihedral_angle_1_deg	6.867
r_angle_refined_deg	1.68
r_angle_other_deg	1.452
r_nbd_other	0.252
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.212
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.17
r_ncsr_local_group_1	0.158
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2443
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	94

Software

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