9RJ4 | pdb_00009rj4

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, 18% PEG3350, 0.1 M calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.79

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 PILATUS3 6M		2024-04-27	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	1.85	111.54	95.3	0.998	14.2	2.1		61085

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	1.85	1.89			0.667

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	1.85	66.2	61078	3026	95.167	0.188	0.1864	0.1955	0.2235	0.2297	46.675

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]
1.125		-0.613	-0.318		-0.502

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.052
r_dihedral_angle_6_deg	15.388
r_lrange_other	13.946
r_lrange_it	13.91
r_scangle_it	13.155
r_scangle_other	13.154
r_dihedral_angle_3_deg	12.145
r_scbond_other	11.502
r_scbond_it	11.501
r_dihedral_angle_other_2_deg	8.742

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.052
r_dihedral_angle_6_deg	15.388
r_lrange_other	13.946
r_lrange_it	13.91
r_scangle_it	13.155
r_scangle_other	13.154
r_dihedral_angle_3_deg	12.145
r_scbond_other	11.502
r_scbond_it	11.501
r_dihedral_angle_other_2_deg	8.742
r_mcangle_other	8.513
r_mcangle_it	8.51
r_mcbond_it	7.65
r_mcbond_other	7.647
r_dihedral_angle_1_deg	5.497
r_angle_refined_deg	1.346
r_angle_other_deg	0.449
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.182
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_other	0.141
r_metal_ion_refined	0.106
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.066
r_ncsr_local_group_1	0.063
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	5409
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	100

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.