9RFL | pdb_00009rfl

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
2.13	42.24

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	1.3	41.62	89.9	0.046	0.055	0.999	18.5	6.2		54497

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	1.3	1.32	92.8		1.088	1.331	0.853	1.9	6

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	1.3	41.62	53973	2769	88.7	0.17	0.1692	0.1762	0.1889	0.1947	14.645

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]
-0.027		-0.049	-0.013		0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.462
r_dihedral_angle_4_deg	22.519
r_dihedral_angle_3_deg	12.347
r_dihedral_angle_1_deg	6.996
r_lrange_it	5.014
r_lrange_other	5.014
r_scangle_it	3.967
r_scangle_other	3.966
r_mcangle_other	2.618
r_mcangle_it	2.614

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.462
r_dihedral_angle_4_deg	22.519
r_dihedral_angle_3_deg	12.347
r_dihedral_angle_1_deg	6.996
r_lrange_it	5.014
r_lrange_other	5.014
r_scangle_it	3.967
r_scangle_other	3.966
r_mcangle_other	2.618
r_mcangle_it	2.614
r_scbond_it	2.583
r_scbond_other	2.582
r_angle_refined_deg	1.927
r_mcbond_it	1.722
r_mcbond_other	1.709
r_angle_other_deg	1.474
r_nbd_refined	0.233
r_symmetry_nbd_other	0.196
r_symmetry_nbd_refined	0.195
r_nbd_other	0.18
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.068
r_bond_refined_d	0.014
r_gen_planes_refined	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	2053
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	26

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.