8CE6

Crystal structure of human Cd11b I domain in P212121 space group

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.15M ammonium sulfate 25% PEG4000 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.482	α = 90
b = 50.906	β = 90
c = 101.399	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 EIGER2 XE 16M		2022-04-08	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	1.575	50.7	91.5	0.999	16.5	11.7		26352

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	1.575	1.696			0.711

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.582	50.7	26237	1288	91.549	0.176	0.1747	0.19	0.2084	0.21	24.32

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]
1.87			-0.64		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.556
r_dihedral_angle_4_deg	13.017
r_dihedral_angle_3_deg	11.751
r_dihedral_angle_1_deg	6.786
r_lrange_it	6.604
r_lrange_other	6.548
r_scangle_it	5.303
r_scangle_other	5.301
r_scbond_it	3.699
r_scbond_other	3.697
r_mcangle_other	2.627
r_mcangle_it	2.626
r_mcbond_it	1.875
r_mcbond_other	1.869
r_angle_refined_deg	1.685
r_angle_other_deg	1.436
r_nbd_refined	0.212
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.172
r_nbd_other	0.147
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbd_refined	0.107
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1572
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	78

Software

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