9CDS | pdb_00009cds

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FJ1

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	15 mg/mL, 0.1 M Magnesium Acetate tetrahydrate and 10% (w/v) PEG 3350; cryo 25%(v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Symmetry
Space Group	P 61

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		2023-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9537	CLSI	08ID-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	1.85	68.86	100	0.125	0.129	0.029	0.999	17	19.4		139556

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	1.85	1.88	100		2.821	2.889	0.661	0.304	1	18.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.85	59.1	139278	6937	99.985	0.204	0.2023	0.1932	0.2333	0.2261	Random	40.945

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]
-2.614			-2.614		5.227

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.678
r_dihedral_angle_3_deg	14.778
r_dihedral_angle_6_deg	14.06
r_dihedral_angle_1_deg	7.087
r_lrange_it	3.895
r_lrange_other	3.885
r_mcangle_it	2.251
r_mcangle_other	2.251
r_scangle_it	2.209
r_scangle_other	2.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.678
r_dihedral_angle_3_deg	14.778
r_dihedral_angle_6_deg	14.06
r_dihedral_angle_1_deg	7.087
r_lrange_it	3.895
r_lrange_other	3.885
r_mcangle_it	2.251
r_mcangle_other	2.251
r_scangle_it	2.209
r_scangle_other	2.209
r_mcbond_it	1.604
r_mcbond_other	1.604
r_scbond_it	1.592
r_scbond_other	1.592
r_angle_refined_deg	1.282
r_angle_other_deg	0.452
r_symmetry_nbd_other	0.205
r_nbd_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.184
r_xyhbond_nbd_refined	0.182
r_ncsr_local_group_3	0.175
r_nbtor_refined	0.17
r_ncsr_local_group_2	0.149
r_nbd_other	0.142
r_ncsr_local_group_1	0.136
r_symmetry_nbtor_other	0.084
r_symmetry_nbd_refined	0.073
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.062
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10205
Nucleic Acid Atoms
Solvent Atoms	563
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.

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