8FIF | pdb_00008fif

A2.3 Nanobody In Complex With Microcystin-LR

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	25% w/v PEG MME 3350, 200 mM ammonium sulfate, 100 mM HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.097	α = 90
b = 101.317	β = 90
c = 102.412	γ = 90

Symmetry
Space Group	P 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 6M		2018-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979460	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.35	36.01	99.1	0.067	0.082	0.046	0.998	12.9	5.4		17031

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43			0.997	0.68

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	35.685	16990	847	98.693	0.238	0.2357	0.24	0.2801	0.28	0.05	60.214

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]
0.013			0.125		-0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.555
r_lrange_it	17.119
r_lrange_other	17.115
r_dihedral_angle_6_deg	15.529
r_scangle_it	11.001
r_scangle_other	10.999
r_mcangle_it	9.66
r_mcangle_other	9.659
r_dihedral_angle_1_deg	9.415
r_dihedral_angle_2_deg	9.127
r_scbond_it	7.561
r_scbond_other	7.559
r_mcbond_it	7.2
r_mcbond_other	7.198
r_angle_refined_deg	1.92
r_angle_other_deg	0.657
r_nbd_refined	0.278
r_xyhbond_nbd_refined	0.275
r_symmetry_nbd_other	0.242
r_symmetry_xyhbond_nbd_refined	0.22
r_nbd_other	0.2
r_nbtor_refined	0.195
r_symmetry_xyhbond_nbd_other	0.188
r_symmetry_nbd_refined	0.147
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.078
r_xyhbond_nbd_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2768
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	213

Software

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