Experiment: 9THU

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AN1

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	40% MPD, 5% PEG 8000, 100 mM sodium cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.24

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 EIGER2 XE 16M		2025-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.691	Diamond	I04

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.4	60.44	100	0.087	0.094	0.035	0.999	11.3	13.9		134250

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.42	100		1.997	2.167	0.838	0.609	1.2	13

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.4	60.44	134158	6674	99.993	0.123	0.122	0.1205	0.1447	0.144	RANDOM	21.904

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]
-0.711			0.921		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.925
r_lrange_it	13.801
r_lrange_other	12.453
r_dihedral_angle_3_deg	11.559
r_scangle_it	10.91
r_scangle_other	10.467
r_scbond_it	8.085
r_scbond_other	7.668
r_dihedral_angle_1_deg	7.105
r_dihedral_angle_2_deg	6.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.925
r_lrange_it	13.801
r_lrange_other	12.453
r_dihedral_angle_3_deg	11.559
r_scangle_it	10.91
r_scangle_other	10.467
r_scbond_it	8.085
r_scbond_other	7.668
r_dihedral_angle_1_deg	7.105
r_dihedral_angle_2_deg	6.578
r_mcangle_other	6.348
r_mcangle_it	6.344
r_mcbond_it	4.845
r_mcbond_other	4.825
r_rigid_bond_restr	4.267
r_angle_refined_deg	1.911
r_angle_other_deg	0.66
r_nbd_other	0.395
r_symmetry_nbd_refined	0.321
r_nbd_refined	0.218
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.166
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.106
r_metal_ion_refined	0.101
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3862
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	50

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.

9THU | pdb_00009thu