8CE9

Crystal structure of human Cd11b I domain in C121 space group

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	25% PEG Smear Medium 0.1M cacodylate pH 5.5 0.2M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.495	α = 90
b = 51.494	β = 132.961
c = 90.172	γ = 90

Symmetry
Space Group	C 1 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 EIGER2 XE 16M		2022-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.11	65.99	92.5	0.981	7.5	6.4		23208

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	2.11	2.15			0.298

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.11	65.989	23208	1085	92.458	0.191	0.1883	0.2389	31.606

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]
1.069		1.006	-2.663		-0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.424
r_dihedral_angle_3_deg	14.443
r_dihedral_angle_4_deg	14.313
r_dihedral_angle_1_deg	7.295
r_lrange_it	6.101
r_lrange_other	6.097
r_scangle_it	4.557
r_scangle_other	4.556
r_mcangle_it	3.284
r_mcangle_other	3.281
r_scbond_it	3.156
r_scbond_other	3.155
r_mcbond_it	2.324
r_mcbond_other	2.321
r_angle_refined_deg	1.609
r_angle_other_deg	1.283
r_nbd_other	0.211
r_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.167
r_nbtor_refined	0.164
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2974
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	105

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing