8K40 | pdb_00008k40

mercuric reductase,GbsMerA, - FAD bound

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		295	1.6 M sodium phosphate monobasic/0.4 M potassium phosphate dibasic, 0.1 M sodium phosphate dibasic/citric acid (pH 4.2)]

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.19	α = 90
b = 105.82	β = 90
c = 126.82	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 9M		2021-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9794	PAL/PLS	5C (4A)

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	2.6	29.38	99.9	0.11	1	15.5	13.2		33032

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	2.6	2.72			1.6	0.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	29.38	33028	2000	99.885	0.223	0.2192	0.22	0.2818	0.28	78.656

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]
-0.021			0.034		-0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.062
r_dihedral_angle_3_deg	17.732
r_dihedral_angle_4_deg	15.865
r_lrange_other	13.615
r_lrange_it	13.614
r_mcangle_it	9.228
r_mcangle_other	9.227
r_scangle_it	8.857
r_scangle_other	8.856
r_dihedral_angle_1_deg	7.057
r_mcbond_it	6.355
r_mcbond_other	6.355
r_scbond_it	5.806
r_scbond_other	5.805
r_angle_refined_deg	1.502
r_angle_other_deg	1.221
r_symmetry_xyhbond_nbd_refined	0.24
r_nbd_other	0.21
r_nbd_refined	0.197
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.061
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	6798
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
MOLREP	phasing