Experiment: 9SMV

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8HHD

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	HEPES 0.1M pH=7.5, 0.2M NaCl 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.97

Symmetry
Space Group	P 1

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		2025-04-09	M	SINGLE WAVELENGTH

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

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	41.643	95	0.997	9	3.5		91656

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	94		0.51

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	1.6	41.643	91625	4692	95.031	0.184	0.1826	0.1932	0.213	0.2204	21.586

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]
-0.283	-0.087	0.786	0.143	1.29	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.766
r_dihedral_angle_3_deg	12.537
r_dihedral_angle_2_deg	9.047
r_dihedral_angle_1_deg	6.535
r_lrange_it	5.164
r_lrange_other	5.08
r_scangle_it	3.81
r_scangle_other	3.81
r_scbond_it	2.453
r_scbond_other	2.453

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.766
r_dihedral_angle_3_deg	12.537
r_dihedral_angle_2_deg	9.047
r_dihedral_angle_1_deg	6.535
r_lrange_it	5.164
r_lrange_other	5.08
r_scangle_it	3.81
r_scangle_other	3.81
r_scbond_it	2.453
r_scbond_other	2.453
r_mcangle_it	2.37
r_mcangle_other	2.37
r_angle_refined_deg	1.701
r_mcbond_it	1.571
r_mcbond_other	1.569
r_angle_other_deg	0.599
r_nbd_refined	0.216
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.154
r_nbd_other	0.146
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.079
r_metal_ion_refined	0.065
r_symmetry_nbd_refined	0.034
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5134
Nucleic Acid Atoms
Solvent Atoms	467
Heterogen Atoms	93

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9SMV | pdb_00009smv