9S89 | pdb_00009s89

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H7S

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	282	20% PEG3350, 0.2 M potassium thiocyanate and 0.1 M Hepes pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.4

Symmetry
Space Group	P 31 2 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 EIGER2 XE 16M		2021-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	2	41.15	100	0.08	0.08	0.018	1	19.6	20.5		29917			49

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	2	2.05	100		1.96	2.01	0.436	0.76	1.9	21.1

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	2	38.602	29881	1465	99.98	0.206	0.205	0.2117	0.2293	0.2333	48.992

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]
-0.538	-0.269		-0.538		1.746

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.074
r_dihedral_angle_3_deg	15.952
r_dihedral_angle_6_deg	15.317
r_scangle_it	7.887
r_scangle_other	7.885
r_lrange_it	7.801
r_lrange_other	7.796
r_dihedral_angle_1_deg	6.239
r_scbond_it	5.795
r_scbond_other	5.794

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.074
r_dihedral_angle_3_deg	15.952
r_dihedral_angle_6_deg	15.317
r_scangle_it	7.887
r_scangle_other	7.885
r_lrange_it	7.801
r_lrange_other	7.796
r_dihedral_angle_1_deg	6.239
r_scbond_it	5.795
r_scbond_other	5.794
r_mcangle_other	5.713
r_mcangle_it	5.705
r_mcbond_other	4.525
r_mcbond_it	4.524
r_angle_refined_deg	1.537
r_angle_other_deg	0.53
r_nbd_other	0.258
r_symmetry_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_refined	0.212
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.162
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2221
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	16

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.