9R3F | pdb_00009r3f

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ELO

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	Protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5 % glycerol, 2 mM TCEP, pH 7, 5 mM lysine Reservoir: 25% PEG 3350, 0.2 M Li sulfate, 0.1 M tris pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.62

Symmetry
Space Group	P 2 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	CCD	RIGAKU SATURN 944+		2019-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5417

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	46.924	99.1	0.174	0.066	0.985	10.1	13.5		54785

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.37	96.9		0.414	0.208	0.957	3.7	9.1

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	2.3	46.924	54729	2695	98.896	0.216	0.2137	0.2184	0.2612	0.2639	14.704

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]
-0.87			1.03		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.98
r_dihedral_angle_3_deg	13.068
r_dihedral_angle_2_deg	8.296
r_dihedral_angle_1_deg	6.992
r_lrange_it	4.913
r_lrange_other	4.781
r_scangle_other	3.451
r_scangle_it	3.45
r_mcangle_it	2.481
r_mcangle_other	2.481

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.98
r_dihedral_angle_3_deg	13.068
r_dihedral_angle_2_deg	8.296
r_dihedral_angle_1_deg	6.992
r_lrange_it	4.913
r_lrange_other	4.781
r_scangle_other	3.451
r_scangle_it	3.45
r_mcangle_it	2.481
r_mcangle_other	2.481
r_scbond_other	2.127
r_scbond_it	2.126
r_angle_refined_deg	1.673
r_mcbond_it	1.543
r_mcbond_other	1.543
r_dihedral_angle_other_2_deg	0.976
r_angle_other_deg	0.578
r_nbd_refined	0.21
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.178
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.169
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbd_refined	0.107
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8053
Nucleic Acid Atoms
Solvent Atoms	796
Heterogen Atoms	83

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.