10AP | pdb_000010ap

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		previously determined WRN structure

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	co-crystallization additive 46 [Proplex-E2-B4+29% glycerol]

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.91

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 EIGER2 S 9M		2022-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.58	46.08	99.8	0.11	0.044	0.999	19.3	13.2		19421

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	2.58	2.69	99.8		1.284	0.377	0.744

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	2.58	46.08	18463	891	99.63	0.23588	0.23351	0.2361	0.28568	0.2867	RANDOM	66.334

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]
0.21			0.88		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.101
r_dihedral_angle_3_deg	13.394
r_dihedral_angle_4_deg	11.722
r_dihedral_angle_1_deg	5.285
r_long_range_B_refined	4.698
r_long_range_B_other	4.685
r_mcangle_it	2.954
r_mcangle_other	2.953
r_scangle_other	2.475
r_mcbond_it	1.661

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.101
r_dihedral_angle_3_deg	13.394
r_dihedral_angle_4_deg	11.722
r_dihedral_angle_1_deg	5.285
r_long_range_B_refined	4.698
r_long_range_B_other	4.685
r_mcangle_it	2.954
r_mcangle_other	2.953
r_scangle_other	2.475
r_mcbond_it	1.661
r_mcbond_other	1.661
r_scbond_it	1.403
r_scbond_other	1.403
r_angle_refined_deg	1.195
r_angle_other_deg	1.142
r_chiral_restr	0.206
r_gen_planes_other	0.009
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.003
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	3357
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	87

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.