9XYL | pdb_00009xyl

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DDU

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.48

Symmetry
Space Group	P 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 EIGER X 9M		2024-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

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	1.81	29.68	83.3	0.07	0.1	0.07	0.99	5.2	1.8		286151			22.5

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	1.81	1.93	53.3		0.371	0.524	0.371	0.62		1.8

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.81	29.68	286150	14477	74.078	0.194	0.1907	0.1898	0.2489	0.2479	25.592

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]
0.329	0.078	0.185	-0.566	0.008	0.231

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.82
r_dihedral_angle_6_deg	15.504
r_dihedral_angle_2_deg	13.757
r_dihedral_angle_1_deg	8.065
r_lrange_it	4.884
r_lrange_other	4.864
r_scangle_it	3.676
r_scangle_other	3.676
r_angle_refined_deg	2.617
r_scbond_it	2.518

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.82
r_dihedral_angle_6_deg	15.504
r_dihedral_angle_2_deg	13.757
r_dihedral_angle_1_deg	8.065
r_lrange_it	4.884
r_lrange_other	4.864
r_scangle_it	3.676
r_scangle_other	3.676
r_angle_refined_deg	2.617
r_scbond_it	2.518
r_scbond_other	2.517
r_mcangle_it	2.49
r_mcangle_other	2.49
r_mcbond_it	1.794
r_mcbond_other	1.787
r_angle_other_deg	0.866
r_symmetry_xyhbond_nbd_refined	0.266
r_nbd_other	0.258
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.22
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.197
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.124
r_symmetry_xyhbond_nbd_other	0.111
r_symmetry_nbtor_other	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34038
Nucleic Acid Atoms
Solvent Atoms	1747
Heterogen Atoms	281

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.

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