4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UQY	PDB ENTRY 3UQY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.9	298	12% PEG4000, 0.1M NaCl, 0.1M NaAc, 0.2M NH4Ac, 0.001M DTT, 0.02% DDM, Tris/HCl, 0.0003M NQNO (a menaquinone analog), pH 5.9, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126	α = 90
b = 165.3	β = 90
c = 212.8	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	PSI PILATUS 6M		2012-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97908	ESRF	ID29

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	3.2	49.12	97.8	0.08	11.35		73321	138472		-3	89.561

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	3.2	3.3	97.1		1.054	1.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3UQY	3.3	25	67491	66832	3298	99.27	0.2018	0.2018	0.1999	0.236	RANDOM	105.957

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]
7.45			-6.89		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.949
r_dihedral_angle_3_deg	17.099
r_dihedral_angle_4_deg	15.385
r_dihedral_angle_1_deg	5.28
r_scangle_it	3.834
r_scbond_it	2.306
r_mcangle_it	1.661
r_angle_refined_deg	1.161
r_mcbond_it	0.837
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.949
r_dihedral_angle_3_deg	17.099
r_dihedral_angle_4_deg	15.385
r_dihedral_angle_1_deg	5.28
r_scangle_it	3.834
r_scbond_it	2.306
r_mcangle_it	1.661
r_angle_refined_deg	1.161
r_mcbond_it	0.837
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30002
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	316

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.