9HMH | pdb_00009hmh

Crystal structure of the Calf domains of Integrin Alpha5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1M Bistris pH 5.5, 0.2M MgCl2, 25% PEG 3350 (wt/vol)

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.016	α = 90
b = 71.437	β = 90
c = 121.266	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 PILATUS3 2M		2018-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	1.0	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.92	46.28	99.5	0.15	0.995	5.47	19.8		33875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.05	91		1.62	0.14	0.8

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	1.92	46.28	33797	1995	99.485	0.225	0.2218	0.2218	0.2822	0.2824	50.54

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]
-3.034			3.139		-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	31.124
r_lrange_other	30.996
r_dihedral_angle_3_deg	17.715
r_dihedral_angle_2_deg	16.935
r_dihedral_angle_6_deg	16.29
r_scangle_it	11.125
r_scangle_other	11.123
r_dihedral_angle_1_deg	10.222
r_mcangle_it	8.803
r_mcangle_other	8.802
r_scbond_it	7.777
r_scbond_other	7.775
r_mcbond_it	6.424
r_mcbond_other	6.424
r_angle_refined_deg	1.944
r_angle_other_deg	0.757
r_symmetry_nbd_refined	0.278
r_xyhbond_nbd_refined	0.258
r_nbd_refined	0.223
r_nbd_other	0.209
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.123
r_chiral_restr	0.103
r_symmetry_xyhbond_nbd_other	0.093
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2528
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms

Software

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