Experiment: 38HK

X-RAY DIFFRACTION

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

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	45.9	99.9	0.154	0.048	0.971	12.6	11.6		10939			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	2.69	99.5		0.401	0.132	0.899	3.8	9.1

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	2.603	45.9	10899	567	99.5	0.191	0.189	0.1893	0.228	0.2306	29.4

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]
-3.49			-0.536		4.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.326
r_dihedral_angle_6_deg	14.064
r_lrange_it	7.77
r_dihedral_angle_1_deg	7.709
r_dihedral_angle_2_deg	6.143
r_scangle_it	5.82
r_scbond_it	3.617
r_mcangle_it	3.49
r_mcbond_it	2.147
r_angle_refined_deg	1.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.326
r_dihedral_angle_6_deg	14.064
r_lrange_it	7.77
r_dihedral_angle_1_deg	7.709
r_dihedral_angle_2_deg	6.143
r_scangle_it	5.82
r_scbond_it	3.617
r_mcangle_it	3.49
r_mcbond_it	2.147
r_angle_refined_deg	1.538
r_nbtor_refined	0.31
r_symmetry_nbd_refined	0.279
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.118
r_symmetry_xyhbond_nbd_refined	0.103
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2452
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms

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.

38HK | pdb_000038hk