6FPW

Structure of fully reduced Hydrogenase (Hyd-1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LMM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	296	100 mM bis-tris pH 5.7 200 mM LiSO4 150 mM NaCl 19-22% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.835	α = 90
b = 97.729	β = 90
c = 182.911	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 PILATUS3 6M		2017-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.35	97.7	100	0.113	7.8	7		366570

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37	100		1.16	1.3	6.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LMM	1.35	91.46	348247	18090	99.9	0.116	0.114	0.144	RANDOM	16.78

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			-0.11		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.511
r_sphericity_free	21.801
r_dihedral_angle_4_deg	16.168
r_dihedral_angle_3_deg	12.083
r_sphericity_bonded	6.867
r_dihedral_angle_1_deg	5.956
r_rigid_bond_restr	2.806
r_long_range_B_refined	2.789
r_scangle_other	2.63
r_long_range_B_other	2.548
r_scbond_it	2.356
r_scbond_other	2.356
r_angle_refined_deg	1.661
r_mcangle_it	1.58
r_mcangle_other	1.58
r_mcbond_it	1.342
r_mcbond_other	1.342
r_angle_other_deg	1.057
r_chiral_restr	0.116
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13165
Nucleic Acid Atoms
Solvent Atoms	1272
Heterogen Atoms	101

Software

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