7Q19 | pdb_00007q19

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#3)

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	2.40 M (NH4)2SO4, 0.5 M Tris-HCl pH 8.5, desipramine

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.298	α = 90
b = 66.298	β = 90
c = 60.63	γ = 120

Symmetry
Space Group	P 3 2 1

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 PILATUS3 6M		2019-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91840	BESSY	14.1

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	1.55	41.69	99.9	0.051	1	23.24	10.3		22796

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	1.55	1.64	99.4		1.022	0.087	1.98	9.11

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	1.55	41.69	22796	1000	99.917	0.199	0.1971	0.21	0.2337	0.24	29.44

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]
0.512	0.256		0.512		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.606
r_dihedral_angle_3_deg	14.175
r_dihedral_angle_1_deg	6.88
r_lrange_it	6.169
r_lrange_other	6.165
r_scangle_other	3.658
r_scangle_it	3.639
r_dihedral_angle_4_deg	3.015
r_mcangle_it	2.659
r_mcangle_other	2.657
r_scbond_other	2.32
r_scbond_it	2.309
r_mcbond_other	1.633
r_mcbond_it	1.632
r_angle_refined_deg	1.629
r_angle_other_deg	1.385
r_nbd_other	0.202
r_nbd_refined	0.196
r_symmetry_nbd_other	0.196
r_symmetry_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1254
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	37

Software

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