Experiment: 9M62

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YL4

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	PEG1500, 100 mM potassium phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.64

Symmetry
Space Group	P 1 21 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 PILATUS4 X 1M		2023-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.033200	SLS	X06SA

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	1.22	39.37	95.9	0.042	0.06	0.042	0.992	9.4	2.3		61638

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	1.22	1.24	99		0.279	0.387	0.268	0.557	2	2.2

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	1.22	33.727	61615	3177	95.557	0.182	0.1808	0.1899	0.2112	0.2208	12.23

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]
1.202		-0.057	-1.044		-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.804
r_dihedral_angle_2_deg	12.947
r_dihedral_angle_3_deg	12.702
r_lrange_it	9.668
r_lrange_other	8.79
r_dihedral_angle_1_deg	7.166
r_rigid_bond_restr	3.041
r_angle_refined_deg	1.947
r_scangle_it	1.578
r_scangle_other	1.457

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.804
r_dihedral_angle_2_deg	12.947
r_dihedral_angle_3_deg	12.702
r_lrange_it	9.668
r_lrange_other	8.79
r_dihedral_angle_1_deg	7.166
r_rigid_bond_restr	3.041
r_angle_refined_deg	1.947
r_scangle_it	1.578
r_scangle_other	1.457
r_scbond_it	1.089
r_mcangle_other	1.047
r_mcangle_it	1.046
r_scbond_other	0.967
r_mcbond_it	0.642
r_mcbond_other	0.638
r_angle_other_deg	0.636
r_xyhbond_nbd_refined	0.27
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.221
r_xyhbond_nbd_other	0.211
r_symmetry_nbd_other	0.199
r_symmetry_xyhbond_nbd_refined	0.199
r_nbd_other	0.184
r_nbtor_refined	0.175
r_metal_ion_refined	0.168
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.011
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	1832
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	7

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.

9M62 | pdb_00009m62