8RXI | pdb_00008rxi

Desulfovibrio desulfuricans [FeFe] hydrogenase in Hinact state derivatized with krypton

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293	1 M Lithium chloride, 0.1 M Sodium acetate, 40 % Polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.6	α = 90
b = 87.967	β = 90
c = 89.71	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 EIGER2 X CdTe 16M		2023-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.861	ESRF	ID23-1

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	1.477	44.895	99.3	0.108	0.123	0.057	0.997	10.9	8.8		66193

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	1.48	1.5	86.1		1.327	1.505	0.7	0.658	1.4	8.5

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	NONE	1.477	44.895	66118	3301	99.279	0.156	0.1542	0.1525	0.1811	0.1794	17.501

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]
0.61			-0.911		0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.263
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_2_deg	8.005
r_dihedral_angle_1_deg	6.445
r_lrange_it	4.347
r_lrange_other	4.257
r_scangle_it	3.294
r_scangle_other	3.293
r_scbond_it	2.309
r_scbond_other	2.308
r_mcangle_it	2.113
r_mcangle_other	2.113
r_angle_refined_deg	2.106
r_mcbond_it	1.505
r_mcbond_other	1.505
r_angle_other_deg	0.661
r_symmetry_nbd_refined	0.296
r_nbd_refined	0.232
r_nbd_other	0.232
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.137
r_metal_ion_refined	0.114
r_symmetry_nbtor_other	0.079
r_xyhbond_nbd_other	0.025
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3707
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	54

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling