9RJ2 | pdb_00009rj2

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES pH 7.0, 20% PEG3350, 0.1 M calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS3 6M		2023-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965	ESRF	MASSIF-1

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	2.3	47.52	98.3	0.998	11.5	3.9		33190

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	2.3	2.38			0.703

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	42.494	33150	913	97.589	0.201	0.1995	0.2093	0.2486	0.2491	66.306

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]
0.323			-5.617		5.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.875
r_dihedral_angle_3_deg	13.336
r_lrange_other	10.784
r_lrange_it	10.783
r_dihedral_angle_2_deg	10.019
r_dihedral_angle_1_deg	7.237
r_scangle_it	7.131
r_scangle_other	7.13
r_mcangle_it	5.487
r_mcangle_other	5.487

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.875
r_dihedral_angle_3_deg	13.336
r_lrange_other	10.784
r_lrange_it	10.783
r_dihedral_angle_2_deg	10.019
r_dihedral_angle_1_deg	7.237
r_scangle_it	7.131
r_scangle_other	7.13
r_mcangle_it	5.487
r_mcangle_other	5.487
r_scbond_it	4.798
r_scbond_other	4.797
r_mcbond_it	3.73
r_mcbond_other	3.73
r_angle_refined_deg	1.539
r_angle_other_deg	0.518
r_symmetry_xyhbond_nbd_refined	0.388
r_symmetry_nbd_refined	0.242
r_nbd_refined	0.214
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.182
r_nbd_other	0.166
r_ncsr_local_group_1	0.085
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5597
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	82

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.