8BAT | pdb_00008bat

Geobacter lovleyi NADAR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold2 model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.15 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% (w/v) PEG 5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.279	α = 90
b = 81.597	β = 90
c = 86.63	γ = 90

Symmetry
Space Group	P 21 2 21

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		2022-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	Diamond	I03

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	2.3	59.468	100	0.173	0.21	0.087	0.994	6.2	5.6		12984

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	2.3	2.38	100		1.475	1.636	0.699	0.557	1	5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	AlphaFold2 model	2.3	59.468	12957	613	99.931	0.183	0.1807	0.19	0.2321	0.23	43.149

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]
-2.891			0.865		2.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.781
r_dihedral_angle_6_deg	15.474
r_dihedral_angle_2_deg	14.006
r_lrange_it	8.884
r_lrange_other	8.88
r_scangle_it	7.349
r_scangle_other	7.346
r_dihedral_angle_1_deg	6.964
r_mcangle_other	5.78
r_mcangle_it	5.777
r_scbond_it	5.11
r_scbond_other	5.107
r_mcbond_it	4.143
r_mcbond_other	4.141
r_angle_refined_deg	1.954
r_angle_other_deg	0.615
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.201
r_nbd_other	0.198
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.187
r_symmetry_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1749
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing