6Z4V | pdb_00006z4v

X-RAY DIFFRACTION

Serial Crystallography (SX)

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293.15	100 mM MES 350-450 mM ammonium tartrate 30% (v/v) PEG400 10 uM NTS8-13

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

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	100	PIXEL	DECTRIS EIGER X 16M		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000009	SLS	X06SA

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

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	2.595	29.251	88.9	0.453	0.484	0.165	0.921	4.3	8.5		14177

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	2.595	2.802			2.576	2.76	0.97	0.458	1.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6YVR	2.595	29.251	14177	723	80.492	0.256	0.2556	0.2573	0.2723	0.2688	33.074

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]
0.276		-0.547	1.332		-1.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.61
r_dihedral_angle_3_deg	15.596
r_dihedral_angle_4_deg	15.293
r_dihedral_angle_1_deg	5.631
r_lrange_it	5.607
r_lrange_other	5.607
r_mcangle_it	2.061
r_mcangle_other	2.061
r_scangle_it	2.028
r_scangle_other	2.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.61
r_dihedral_angle_3_deg	15.596
r_dihedral_angle_4_deg	15.293
r_dihedral_angle_1_deg	5.631
r_lrange_it	5.607
r_lrange_other	5.607
r_mcangle_it	2.061
r_mcangle_other	2.061
r_scangle_it	2.028
r_scangle_other	2.027
r_angle_refined_deg	1.216
r_mcbond_it	1.215
r_mcbond_other	1.214
r_angle_other_deg	1.196
r_scbond_it	1.178
r_scbond_other	1.176
r_symmetry_xyhbond_nbd_refined	0.189
r_nbd_refined	0.188
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.13
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.047
r_symmetry_xyhbond_nbd_other	0.01
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3433
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

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.