Experiment: 9S39

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NJ4

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	heptane-triol, KPi, Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
5.56	77.89

Symmetry
Space Group	P 43 21 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	PSI JUNGFRAU 4M		2024-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.072	ESRF	ID29

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.3	113	100	0.99	6.6	20		72801

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.4	100		0.43		6.6

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	3.3	60	59063	2997	98.946	0.249	0.2462	0.2253	0.2963	0.2772	41.3

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]
1.632			1.632		-3.264

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	21.403
r_lrange_other	21.403
r_dihedral_angle_3_deg	17.944
r_scangle_it	17.566
r_scangle_other	17.565
r_mcangle_other	16.879
r_mcangle_it	16.876
r_dihedral_angle_6_deg	15.878
r_dihedral_angle_2_deg	12.16
r_scbond_it	11.884

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	21.403
r_lrange_other	21.403
r_dihedral_angle_3_deg	17.944
r_scangle_it	17.566
r_scangle_other	17.565
r_mcangle_other	16.879
r_mcangle_it	16.876
r_dihedral_angle_6_deg	15.878
r_dihedral_angle_2_deg	12.16
r_scbond_it	11.884
r_scbond_other	11.883
r_mcbond_it	11.688
r_mcbond_other	11.686
r_dihedral_angle_1_deg	7.597
r_angle_refined_deg	2.285
r_angle_other_deg	0.852
r_symmetry_nbd_refined	0.298
r_nbd_refined	0.232
r_nbd_other	0.204
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.17
r_chiral_restr	0.168
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.08
r_metal_ion_refined	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9291
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	695

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.

9S39 | pdb_00009s39