9XHC | pdb_00009xhc

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.82

Symmetry
Space Group	C 1 2 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 PILATUS 12M		2024-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17UM	0.97918	SSRF	BL17UM

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	48.1	99.3	0.139	0.98	7.8	6.6		23980

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85			0.416	0.7

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7MLF	1.802	48.067	23980	1203	99.148	0.174	0.1709	0.1855	0.2362	0.2446	23.886

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]
1.976		-1.331	0.108		-1.335

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.402
r_dihedral_angle_4_deg	16.797
r_dihedral_angle_3_deg	13.745
r_dihedral_angle_1_deg	7.542
r_lrange_it	7.364
r_lrange_other	7.135
r_scangle_other	4.867
r_scangle_it	4.863
r_mcangle_it	3.299
r_mcangle_other	3.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.402
r_dihedral_angle_4_deg	16.797
r_dihedral_angle_3_deg	13.745
r_dihedral_angle_1_deg	7.542
r_lrange_it	7.364
r_lrange_other	7.135
r_scangle_other	4.867
r_scangle_it	4.863
r_mcangle_it	3.299
r_mcangle_other	3.298
r_scbond_it	3.283
r_scbond_other	3.265
r_dihedral_angle_other_3_deg	2.973
r_mcbond_it	2.281
r_mcbond_other	2.277
r_angle_refined_deg	1.875
r_angle_other_deg	1.487
r_symmetry_xyhbond_nbd_refined	0.336
r_xyhbond_nbd_refined	0.33
r_nbd_other	0.244
r_nbd_refined	0.228
r_symmetry_nbd_refined	0.224
r_symmetry_xyhbond_nbd_other	0.212
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.174
r_xyhbond_nbd_other	0.1
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	38

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.