9SF6 | pdb_00009sf6

Amuc0953 N-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpulished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	20 % PEG 3350, 0.2 M NaI 25 mg/ml protein

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.44	α = 90
b = 59.15	β = 95.11
c = 111.12	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

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		2022-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.8	Diamond	I04

Data Collection

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	55.34	99.9	0.193	0.229	0.121	0.994	6.6	6.9		88190

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)
	2	2.04	99.9		2.063	2.433	1.28	0.364	1.2	7

Refinement

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	2	55.34	88175	4426	99.904	0.194	0.1921	0.202	0.2321	0.2396	44.953

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]
3.878		0.645	-2.079		-1.885

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.793
r_dihedral_angle_3_deg	13.427
r_lrange_it	9.342
r_lrange_other	9.333
r_dihedral_angle_2_deg	8.333
r_scangle_it	7.706
r_scangle_other	7.633
r_dihedral_angle_1_deg	7.572
r_mcangle_other	5.097
r_mcangle_it	5.095
r_scbond_it	4.999
r_scbond_other	4.904
r_mcbond_it	3.558
r_mcbond_other	3.558
r_angle_refined_deg	1.555
r_angle_other_deg	0.539
r_nbd_other	0.223
r_symmetry_nbd_refined	0.21
r_nbd_refined	0.199
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.167
r_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6878
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing