8R8B | pdb_00008r8b

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	291	0.1M Hepes 7.0 2.0M AmSO4

Crystal Properties
Matthews coefficient	Solvent content
4.04	69.53

Symmetry
Space Group	P 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 PILATUS 6M		2021-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979335	ALBA	XALOC

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.808	139.2	95.5	0.99	8.53	3.5		1088963

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.92			0.31

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2YNN	1.808	49.377	879297	44507	72.385	0.16	0.1594	0.1953	0.1744	0.2111	29.659

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]
-0.112	-7.736	-11.265	-2.889	8.738	3.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.728
r_dihedral_angle_4_deg	15.84
r_dihedral_angle_3_deg	15.281
r_dihedral_angle_1_deg	8.121
r_lrange_it	2.821
r_lrange_other	2.669
r_mcangle_it	1.256
r_mcangle_other	1.256
r_angle_refined_deg	1.247
r_angle_other_deg	1.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.728
r_dihedral_angle_4_deg	15.84
r_dihedral_angle_3_deg	15.281
r_dihedral_angle_1_deg	8.121
r_lrange_it	2.821
r_lrange_other	2.669
r_mcangle_it	1.256
r_mcangle_other	1.256
r_angle_refined_deg	1.247
r_angle_other_deg	1.041
r_scangle_it	0.788
r_scangle_other	0.788
r_mcbond_it	0.729
r_mcbond_other	0.729
r_scbond_it	0.478
r_scbond_other	0.478
r_nbd_refined	0.171
r_symmetry_nbd_other	0.171
r_nbd_other	0.159
r_nbtor_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.136
r_xyhbond_nbd_refined	0.125
r_symmetry_nbd_refined	0.122
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.042
r_symmetry_xyhbond_nbd_other	0.034
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	59524
Nucleic Acid Atoms
Solvent Atoms	3348
Heterogen Atoms	1372

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.

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