Experiment: 5NDC

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S8F

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.3	293	100mM sodium cacodylate trihydrate pH 5.3, 37% PEG400, 1.4M NaCl Room temperature for 2-3 days

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.69

Symmetry
Space Group	C 1 2 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	MPCCD		2016-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.6314	SACLA	BL3

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	2.3	36.4	100	0.956	0.1937	3.74	14.7	1864107	50602

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34			0.366	1.2		14.7

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3S8F	2.3	36.4	47055	2511	99.92	0.1635	0.16174	0.19749	0.2166	RANDOM	51.446

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]
-0.49		0.74	-1.19		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.719
r_dihedral_angle_4_deg	20.854
r_dihedral_angle_3_deg	14.321
r_dihedral_angle_1_deg	5.876
r_long_range_B_refined	4.533
r_long_range_B_other	4.533
r_scangle_other	3.138
r_mcangle_it	2.515
r_mcangle_other	2.515
r_scbond_it	1.932

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.719
r_dihedral_angle_4_deg	20.854
r_dihedral_angle_3_deg	14.321
r_dihedral_angle_1_deg	5.876
r_long_range_B_refined	4.533
r_long_range_B_other	4.533
r_scangle_other	3.138
r_mcangle_it	2.515
r_mcangle_other	2.515
r_scbond_it	1.932
r_scbond_other	1.932
r_angle_refined_deg	1.612
r_mcbond_it	1.596
r_mcbond_other	1.595
r_angle_other_deg	0.988
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.002
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	5910
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	384

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.

5NDC | pdb_00005ndc