9YMP | pdb_00009ymp

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6OIM

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	200mM ammonium sulfate, 100mM sodium acetate, 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.23

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2022-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00002	ALS	5.0.2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.12	50	95.9	0.058	0.999	17.04	6.5		133207

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	1.12	1.19	82.5		0.239	0.96	4.86	5.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.12	30	66130	3537	95.86	0.18574	0.18521	0.1942	0.19574	0.2072	RANDOM	13.128

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]
0.22			-0.08		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_4_deg	18.455
r_dihedral_angle_3_deg	12.064
r_dihedral_angle_1_deg	5.789
r_long_range_B_refined	3.433
r_long_range_B_other	3.145
r_scangle_other	1.424
r_angle_refined_deg	1.32
r_angle_other_deg	1.317
r_mcangle_it	1.267

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_4_deg	18.455
r_dihedral_angle_3_deg	12.064
r_dihedral_angle_1_deg	5.789
r_long_range_B_refined	3.433
r_long_range_B_other	3.145
r_scangle_other	1.424
r_angle_refined_deg	1.32
r_angle_other_deg	1.317
r_mcangle_it	1.267
r_mcangle_other	1.266
r_scbond_other	0.874
r_scbond_it	0.873
r_mcbond_it	0.727
r_mcbond_other	0.727
r_chiral_restr	0.054
r_gen_planes_refined	0.01
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1340
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	90

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.