9RZQ | pdb_00009rzq

Crystal structure of Anaplasma phagocytophilum p44-23 outer membrane protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	0.2 M ammonium acetate 0.1 M Tris (8.0) 20% PEG 500

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.63	α = 84.42
b = 43.26	β = 69.41
c = 47.8	γ = 89.99

Symmetry
Space Group	P 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 EIGER2 XE 16M		2023-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.7054	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	44.5	94	0.051	0.999	12.7	3.7		28346

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.74	95.4		0.317	0.938	3.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	44.5	27005	1341	93.96	0.20685	0.20435	0.2156	0.25344	0.2643	RANDOM	27.158

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]
0.53	0.42	1.01	4.44	-2.01	-3.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.823
r_dihedral_angle_3_deg	17.234
r_dihedral_angle_4_deg	12.975
r_rigid_bond_restr	12.481
r_long_range_B_refined	8.405
r_long_range_B_other	8.33
r_scangle_other	7.455
r_dihedral_angle_1_deg	7.198
r_mcangle_it	6.833
r_mcangle_other	6.833
r_scbond_it	6.675
r_scbond_other	6.672
r_mcbond_it	5.732
r_mcbond_other	5.715
r_angle_refined_deg	2.05
r_angle_other_deg	1.426
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2232
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing