8OVQ | pdb_00008ovq

Crystal structure of Geodia cydonium sponge adhesion molecule long form (SAML).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	PEG4000, 0.2M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.08	α = 90
b = 41.16	β = 90.009
c = 77.801	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		2022-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.61	77.8	99.5	0.067	0.088	0.056	0.997	9.3	4.1		27255			20.56

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	1.61	1.64	99.6		0.74	0.576	1.5	3.7

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	1.61	38.931	27237	1317	99.431	0.153	0.1509	0.16	0.2027	0.21	27.475

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]
-0.307		0.021	-1.084		1.391

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.996
r_dihedral_angle_3_deg	11.247
r_dihedral_angle_1_deg	7.359
r_dihedral_angle_2_deg	4.539
r_lrange_it	4.387
r_lrange_other	4.386
r_rigid_bond_restr	4.066
r_mcangle_it	3.199
r_mcangle_other	3.199
r_scangle_it	2.763
r_scangle_other	2.75
r_mcbond_it	2.293
r_mcbond_other	2.289
r_scbond_it	2.052
r_scbond_other	2.046
r_angle_refined_deg	1.554
r_angle_other_deg	0.554
r_xyhbond_nbd_refined	0.227
r_nbd_other	0.225
r_nbd_refined	0.217
r_symmetry_nbd_other	0.214
r_symmetry_nbd_refined	0.207
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.123
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1493
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	75

Software

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