7WKI

Structure of the ultra-affinity complex between CFH and a nanobody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SW0	3SW0, 5LHN
experimental model	PDB	5LHN	3SW0, 5LHN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Phosphate monohydrate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.96	α = 90
b = 75.96	β = 90
c = 143.2	γ = 120

Symmetry
Space Group	P 32 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 S 2M		2020-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.6	48.44	99.9	0.16	0.997	12.3	13.5		15303

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74			0.916	2.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3SW0, 5LHN	2.6	48.44	15281	753	99.876	0.194	0.1921	0.2392	62.83

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]
1.925	0.962		1.925		-6.245

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.987
r_dihedral_angle_4_deg	23.3
r_dihedral_angle_3_deg	18.402
r_dihedral_angle_1_deg	8.689
r_lrange_it	7.154
r_lrange_other	7.152
r_scangle_it	5.572
r_scangle_other	5.571
r_mcangle_other	4.349
r_mcangle_it	4.345
r_scbond_it	3.623
r_scbond_other	3.622
r_mcbond_it	2.82
r_mcbond_other	2.79
r_angle_refined_deg	1.863
r_angle_other_deg	1.345
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.212
r_nbd_other	0.197
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.158
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1985
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing