9N42 | pdb_00009n42

Crystal structure of an anti-CRISPR Protein AcrIE7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9N3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	22% PEG MME 5K, 0.1M BisTris (pH 5.4)

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.501	α = 90
b = 62.077	β = 103.208
c = 87.737	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS EIGER X 16M		2023-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.034	APS	23-ID-B

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	1.5	85.42	98.7	0.073	0.075	0.018	0.999	21.8	32.7		51688			32.52

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	1.51	1.54	98.7		2.813	2.88	0.604	0.696	1.2	21.5

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	1.5	85.416	51687	2590	98.632	0.208	0.2065	0.2066	0.2368	0.237	39.393

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]
-1.406		0.302	0.412		0.768

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.932
r_dihedral_angle_3_deg	14.021
r_dihedral_angle_2_deg	9.54
r_lrange_other	6.813
r_lrange_it	6.809
r_scangle_it	6.221
r_scangle_other	6.22
r_dihedral_angle_1_deg	5.44
r_scbond_it	4.453
r_scbond_other	4.435
r_mcangle_it	3.231
r_mcangle_other	3.23
r_mcbond_it	2.843
r_mcbond_other	2.835
r_angle_refined_deg	2.18
r_angle_other_deg	0.738
r_nbd_refined	0.238
r_nbd_other	0.208
r_symmetry_nbd_refined	0.195
r_nbtor_refined	0.192
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.132
r_ncsr_local_group_2	0.131
r_chiral_restr	0.118
r_symmetry_xyhbond_nbd_refined	0.113
r_ncsr_local_group_3	0.113
r_ncsr_local_group_1	0.104
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2506
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Coot	model building
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
pointless	data scaling
DIALS	data reduction
Blu-Ice	data collection