9WOL | pdb_00009wol

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	291	0.2 M di-Ammonium tartrate (pH 6.6) and 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.49

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2023-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	2.11	48.38	98.6	0.071	0.086	0.048	0.998	15.4	5.9		44654

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	2.11	2.17	86.4		0.206	0.262	0.16	0.952	4.9	4.4

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	THROUGHOUT	2.113	45.948	44621	2240	98.538	0.15	0.1474	0.1579	0.1968	0.201	RANDOM	21.275

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]
0.081		-0.214	0.756		-0.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.757
r_dihedral_angle_6_deg	16.277
r_dihedral_angle_3_deg	13.819
r_dihedral_angle_1_deg	6.34
r_lrange_it	6.277
r_lrange_other	6.226
r_scangle_it	4.325
r_scangle_other	4.325
r_mcangle_it	2.981
r_mcangle_other	2.981

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.757
r_dihedral_angle_6_deg	16.277
r_dihedral_angle_3_deg	13.819
r_dihedral_angle_1_deg	6.34
r_lrange_it	6.277
r_lrange_other	6.226
r_scangle_it	4.325
r_scangle_other	4.325
r_mcangle_it	2.981
r_mcangle_other	2.981
r_scbond_it	2.777
r_scbond_other	2.776
r_mcbond_it	1.961
r_mcbond_other	1.961
r_angle_refined_deg	1.452
r_angle_other_deg	0.491
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.209
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.18
r_nbd_other	0.175
r_metal_ion_refined	0.158
r_symmetry_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5016
Nucleic Acid Atoms
Solvent Atoms	699
Heterogen Atoms	158

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.