6NMV | pdb_00006nmv

Non-Blocking Fab 218 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	285	0.1 M Tris-HCl, 0.2 M MgCl2, 25% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.29	α = 90
b = 76.09	β = 95.26
c = 72.81	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2017-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	.97923	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.61	38.16	98.3	7.5	3.2		45887

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.61	2.68	97.7		0.7	3.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.61	38.16	13589	880	98.19	0.2009	0.1945	0.2	0.3007	0.3	RANDOM	65.411

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]
0.86		-1.16	-3.23		2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.135
r_dihedral_angle_3_deg	19.002
r_dihedral_angle_4_deg	15.44
r_dihedral_angle_1_deg	9.493
r_angle_refined_deg	1.479
r_angle_other_deg	0.862
r_chiral_restr	0.064
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.135
r_dihedral_angle_3_deg	19.002
r_dihedral_angle_4_deg	15.44
r_dihedral_angle_1_deg	9.493
r_angle_refined_deg	1.479
r_angle_other_deg	0.862
r_chiral_restr	0.064
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3939
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.