9N60 | pdb_00009n60

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R6S

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.1 M MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.13

Symmetry
Space Group	P 4 21 2

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 EIGER X 9M		2023-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.920105	NSLS-II	17-ID-1

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	2.47	127.63	100	0.382	0.396	0.104	0.998	10.1	27		35919

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)
	2.47	2.57	100		4.952	5.132	1.348	0.366	0.9	27.7

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	2.47	127.629	35893	1852	99.997	0.216	0.2146	0.2146	0.2431	0.243	56.964

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]
-1.172			-1.172		2.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.343
r_dihedral_angle_6_deg	15.509
r_dihedral_angle_3_deg	15.433
r_lrange_it	15.071
r_scangle_it	14.732
r_scbond_it	13.157
r_mcangle_it	10.342
r_mcbond_it	9.637
r_dihedral_angle_1_deg	6.791
r_angle_refined_deg	1.742

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.343
r_dihedral_angle_6_deg	15.509
r_dihedral_angle_3_deg	15.433
r_lrange_it	15.071
r_scangle_it	14.732
r_scbond_it	13.157
r_mcangle_it	10.342
r_mcbond_it	9.637
r_dihedral_angle_1_deg	6.791
r_angle_refined_deg	1.742
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.144
r_ncsr_local_group_1	0.087
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4597
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	23

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.