12KZ | pdb_000012kz

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	500mM lithium chloride, 100mM TRIS, 30% PEG 6000, 100mM sodium/potassium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.03

Symmetry
Space Group	H 3 2

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		2024-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00000	ALS	5.0.2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.45	50	99.6	0.067	0.999	13.12	5.06		69153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.54	99.1		1.308	0.452	1.15	4.95

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.45	30	34006	1791	99.6	0.18046	0.17993	0.1848	0.18994	0.1934	RANDOM	21.759

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]
-0.14	-0.07		-0.14		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.015
r_dihedral_angle_4_deg	16.89
r_dihedral_angle_3_deg	13.534
r_dihedral_angle_1_deg	5.85
r_long_range_B_refined	4.598
r_long_range_B_other	4.413
r_scangle_other	2.942
r_mcangle_it	2.145
r_mcangle_other	2.145
r_scbond_it	1.828

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.015
r_dihedral_angle_4_deg	16.89
r_dihedral_angle_3_deg	13.534
r_dihedral_angle_1_deg	5.85
r_long_range_B_refined	4.598
r_long_range_B_other	4.413
r_scangle_other	2.942
r_mcangle_it	2.145
r_mcangle_other	2.145
r_scbond_it	1.828
r_scbond_other	1.827
r_angle_refined_deg	1.476
r_angle_other_deg	1.325
r_mcbond_it	1.315
r_mcbond_other	1.31
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1352
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	68

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.