6Z4S | pdb_00006z4s

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 Na citrate 225-460 mM ammonium nitrate 30-32% (v/v) PEG400 1 uM SR48692

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

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 EIGER X 16M		2019-12-08	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	2.707	29.353	90.6	0.525	0.564	0.198	0.964	4.3	7.3		10475

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	2.707	3.029			4.678	4.929	1.504	0.294	1.4

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	2.707	29.353	10474	552	68.408	0.274	0.2727	0.2754	0.2889	0.2953	38.575

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]
0.315			1.193		-1.508

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.948
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_4_deg	12.63
r_dihedral_angle_1_deg	3.868
r_lrange_other	3.389
r_lrange_it	3.387
r_angle_refined_deg	1.165
r_angle_other_deg	1.08
r_mcangle_it	0.976
r_mcangle_other	0.976

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.948
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_4_deg	12.63
r_dihedral_angle_1_deg	3.868
r_lrange_other	3.389
r_lrange_it	3.387
r_angle_refined_deg	1.165
r_angle_other_deg	1.08
r_mcangle_it	0.976
r_mcangle_other	0.976
r_scangle_it	0.572
r_scangle_other	0.572
r_mcbond_it	0.523
r_mcbond_other	0.523
r_scbond_it	0.284
r_scbond_other	0.284
r_nbd_refined	0.167
r_nbtor_refined	0.152
r_symmetry_nbd_other	0.145
r_nbd_other	0.135
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbd_refined	0.117
r_xyhbond_nbd_refined	0.115
r_symmetry_xyhbond_nbd_refined	0.091
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.032
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3288
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

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.