9IHA | pdb_00009iha

A-SPECTRIN SH3 DOMAIN V9L, A11V, M25V, V46F, V58L MUTANT

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	2M Ammonium Sulfate and 0.1M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.021	α = 90
b = 36.562	β = 90
c = 64.926	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	80	PIXEL	DECTRIS PILATUS 6M		2022-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.013	32.463	100	0.059	0.018	0.998	21.7	12.4		40408

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.013	1.03	100		1.689	0.51	0.649	1.5

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	1.013	32.463	40406	2007	99.993	0.163	0.1629	0.1705	0.174	0.1785	18.514

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]
-0.518			0.008		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_rigid_bond_restr	31.377
r_dihedral_angle_4_deg	18.123
r_dihedral_angle_3_deg	12.636
r_scbond_it	7.917
r_dihedral_angle_1_deg	7.184
r_scangle_it	7.125
r_scbond_other	6.475
r_lrange_it	6.011
r_scangle_other	5.757
r_lrange_other	5.654
r_mcangle_other	3.582
r_mcangle_it	3.464
r_mcbond_it	3.041
r_angle_refined_deg	3.008
r_mcbond_other	2.918
r_angle_other_deg	1.652
r_symmetry_nbd_refined	0.483
r_nbd_other	0.329
r_nbd_refined	0.269
r_xyhbond_nbd_refined	0.238
r_symmetry_xyhbond_nbd_refined	0.231
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.182
r_xyhbond_nbd_other	0.148
r_chiral_restr	0.12
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.033
r_gen_planes_refined	0.014
r_bond_other_d	0.009
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	525
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	10

Software

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