3VX3

Crystal structure of [NiFe] hydrogenase maturation protein HypB from Thermococcus kodakarensis KOD1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	1.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.241	α = 90
b = 137.689	β = 90
c = 150.821	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	95	CCD	RAYONIX MX-225		2009-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	50	99.8	0.1		7.1		40492

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	100		0.529	3.6	6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	40.22	38324	2010	99.45	0.19485	0.19362	0.21845	RANDOM	39.133

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]
-1.98			0.22		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.251
r_dihedral_angle_4_deg	17.933
r_dihedral_angle_3_deg	14.838
r_dihedral_angle_1_deg	5.979
r_scangle_it	3.449
r_scbond_it	2.101
r_angle_refined_deg	1.497
r_mcangle_it	1.286
r_mcbond_it	0.699
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.251
r_dihedral_angle_4_deg	17.933
r_dihedral_angle_3_deg	14.838
r_dihedral_angle_1_deg	5.979
r_scangle_it	3.449
r_scbond_it	2.101
r_angle_refined_deg	1.497
r_mcangle_it	1.286
r_mcbond_it	0.699
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3678
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	78

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.