9HDB | pdb_00009hdb

Sla1 SH3_3 domain (residues 355-414)

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	7.5	292	0.1M HEPES pH 7.5 20% PEG 10000 1mM peptide (PVSTPARTPARTPTP) dissolved in 0.03M HEPES pH 8, 0.15M NaCl, 0.5mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.533	α = 90
b = 50.423	β = 90
c = 51.967	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 PILATUS 6M-F		2024-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.49	51.97	100	0.078	0.087	0.037	0.998	15.6	10		17131

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.52	99.9		0.422	0.473	0.211	0.943	4.8	9.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.491	36.214	17083	848	99.947	0.145	0.143	0.1421	0.1895	0.1888	RANDOM	18.897

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]
-0.915			0.226		0.689

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.048
r_dihedral_angle_6_deg	16.885
r_dihedral_angle_3_deg	13.145
r_lrange_it	11.566
r_lrange_other	11.097
r_scangle_it	8.545
r_scangle_other	8.54
r_scbond_it	6.214
r_scbond_other	6.208
r_dihedral_angle_1_deg	6.153
r_mcangle_other	5.995
r_mcangle_it	5.992
r_rigid_bond_restr	5.644
r_mcbond_it	4.4
r_mcbond_other	4.375
r_angle_refined_deg	1.965
r_angle_other_deg	0.664
r_nbd_refined	0.196
r_symmetry_nbd_other	0.194
r_symmetry_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.156
r_nbd_other	0.155
r_ncsr_local_group_1	0.147
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	982
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
autoPROC	data reduction
PHENIX	model building
Coot	model building
MOLREP	phasing