9RFO | pdb_00009rfo

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	296	1.5 M sodium citrate, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.45

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 PILATUS 6M		2023-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.75	42.49	92.3	0.039	0.048	0.999	25.6	5.4		23288

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	91.2		0.144	0.185	0.971	7.5	3.9

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	NONE	1.75	41.95	23258	1232	92.213	0.152	0.1499	0.1633	0.1791	0.1833	15.145

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]
-0.32		0.195	0.417		-0.175

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_4_deg	21.901
r_dihedral_angle_3_deg	13.469
r_dihedral_angle_1_deg	7.156
r_lrange_it	5.276
r_lrange_other	5.275
r_scangle_it	3.765
r_scangle_other	3.763
r_mcangle_other	2.517
r_mcangle_it	2.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_4_deg	21.901
r_dihedral_angle_3_deg	13.469
r_dihedral_angle_1_deg	7.156
r_lrange_it	5.276
r_lrange_other	5.275
r_scangle_it	3.765
r_scangle_other	3.763
r_mcangle_other	2.517
r_mcangle_it	2.515
r_scbond_it	2.382
r_scbond_other	2.381
r_angle_refined_deg	1.755
r_mcbond_it	1.614
r_mcbond_other	1.606
r_angle_other_deg	1.428
r_nbd_refined	0.232
r_symmetry_nbd_other	0.195
r_symmetry_xyhbond_nbd_refined	0.182
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.172
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.066
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	36

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.