3BN3 | pdb_00003bn3

crystal structure of ICAM-5 in complex with aL I domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T0P	PDB IDS 1T0P AND 1IC1
experimental model	PDB	1IC1	PDB IDS 1T0P AND 1IC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	296	0.1M HEPES pH7.5, 7.5%PEG8000, 10%glycerol, 5mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.73	66.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.793	α = 90
b = 71.507	β = 90
c = 143.871	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	CCD				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97931	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2.099	71.98	98.6	0.072	0.054		8.2		37303			33.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.099	2.18	95.5		0.454	0.471	3.76	5.6	3564

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB IDS 1T0P AND 1IC1	2.099	71.98	37303	37303	1863	98.03	0.193	0.193	0.191	0.2	0.235	0.24	RANDOM	43.703

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]
-0.71			4.05		-3.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.189
r_dihedral_angle_4_deg	13.636
r_dihedral_angle_3_deg	13.285
r_dihedral_angle_1_deg	5.929
r_scangle_it	4.104
r_mcangle_it	3.484
r_mcbond_it	2.855
r_scbond_it	2.709
r_angle_refined_deg	1.32
r_angle_other_deg	0.816
r_mcbond_other	0.531
r_symmetry_vdw_other	0.22
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.201
r_nbd_other	0.189
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.105
r_nbtor_other	0.1
r_chiral_restr	0.075
r_metal_ion_refined	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3000
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	97

Software

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