9PLM | pdb_00009plm

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		056 model

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	100 mM NaCl, 100 mM HEPES, pH 7.5, 12 % polyethylene glycol 20,000

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.96

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	99	PIXEL	DECTRIS EIGER2 XE 16M		2025-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979460	SSRL	BL12-2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.2	49.18	74.2	0.065	12.3	6		92180

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22			0.787

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	1.32	49.18	84004	4233	89.494	0.152	0.1503	0.1509	0.1781	0.1771	17.437

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]
2.242			-1.006		-1.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.947
r_dihedral_angle_3_deg	11.713
r_dihedral_angle_2_deg	9.23
r_lrange_it	8.556
r_lrange_other	8.555
r_dihedral_angle_1_deg	6.823
r_scangle_it	4.198
r_scangle_other	4.197
r_scbond_it	2.761
r_scbond_other	2.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.947
r_dihedral_angle_3_deg	11.713
r_dihedral_angle_2_deg	9.23
r_lrange_it	8.556
r_lrange_other	8.555
r_dihedral_angle_1_deg	6.823
r_scangle_it	4.198
r_scangle_other	4.197
r_scbond_it	2.761
r_scbond_other	2.76
r_mcangle_other	2.127
r_mcangle_it	2.125
r_angle_refined_deg	1.911
r_mcbond_it	1.397
r_mcbond_other	1.397
r_angle_other_deg	0.658
r_symmetry_xyhbond_nbd_refined	0.301
r_symmetry_nbd_refined	0.292
r_xyhbond_nbd_refined	0.244
r_nbd_other	0.235
r_nbd_refined	0.23
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.186
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2671
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	68

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.