7HRG | pdb_00007hrg

PanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z104474062

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.85	293	0.1M MES pH 6.85, 1.6M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.595	α = 90
b = 99.614	β = 90
c = 127.835	γ = 90

Symmetry
Space Group	I 2 2 2

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 9M		2023-09-11		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92124	Diamond	I04-1

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	1.92	78.59	99.6	0.176	0.183	0.05	0.998	8.4	13.6		48653

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	1.92	1.96		97.8	1.076	1.117	0.3	0.938		13.8

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	1.92	78.58	44212	2253	95.01	0.3251	0.32277	0.3302	0.37008	0.3699	RANDOM	53.211

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]
0.41			-0.03		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.336
r_dihedral_angle_3_deg	17.347
r_dihedral_angle_4_deg	16.204
r_long_range_B_refined	7.475
r_long_range_B_other	7.446
r_dihedral_angle_1_deg	6.113
r_scangle_other	3.774
r_mcangle_it	3.663
r_mcangle_other	3.663
r_scbond_it	1.71
r_scbond_other	1.705
r_mcbond_other	1.647
r_mcbond_it	1.631
r_angle_refined_deg	1.304
r_angle_other_deg	1.088
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4302
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC5	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction