38HJ | pdb_000038hj

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VBD

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.1	291	0.1 M CHES buffer, pH 9.1 to 10.1, and 32-42% PEG 600

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.5

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 EIGER X 16M		2025-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	39.1	92.6	0.181	0.072	0.968	16.5	6.8		10328			35.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	99.6		0.47	0.185	0.909	1.7

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	FOURIER SYNTHESIS	FREE R-VALUE	2.6	39.1	10292	538	92.587	0.23	0.227	0.2304	0.292	0.2922	42.5

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]
-0.802			-2.775		3.577

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.86
r_dihedral_angle_3_deg	13.927
r_dihedral_angle_2_deg	10.546
r_lrange_it	8.08
r_lrange_other	8.078
r_dihedral_angle_1_deg	7.971
r_scangle_it	6.423
r_scangle_other	6.422
r_mcangle_it	5.318
r_mcangle_other	5.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.86
r_dihedral_angle_3_deg	13.927
r_dihedral_angle_2_deg	10.546
r_lrange_it	8.08
r_lrange_other	8.078
r_dihedral_angle_1_deg	7.971
r_scangle_it	6.423
r_scangle_other	6.422
r_mcangle_it	5.318
r_mcangle_other	5.317
r_scbond_it	4.058
r_scbond_other	4.056
r_mcbond_it	3.558
r_mcbond_other	3.539
r_angle_refined_deg	1.7
r_angle_other_deg	1.544
r_nbd_refined	0.216
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.177
r_nbd_other	0.14
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_refined	0.056
r_symmetry_nbd_refined	0.01
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2452
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	37

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.