5MDJ | pdb_00005mdj

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its as-isolated high-pressurized form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IUB	4IUB/4TTT
experimental model	PDB	4TTT	4IUB/4TTT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	20-30%PEG3350, 0.1M BIS-TRIS ph 5.5-6.5

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.395	α = 90
b = 95.696	β = 90
c = 121.565	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 PILATUS 6M	Mirrors	2016-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	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	1.48	47.85	99.8	0.064	12.5	5.6		142561

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	1.48	1.56	99.4		0.839	2	5.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4IUB/4TTT	1.48	47.85	135294	7173	99.75	0.14398	0.14247	0.15	0.17234	0.18	RANDOM	27.523

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]
-0.08			-0.42		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.361
r_sphericity_free	20.019
r_dihedral_angle_4_deg	18.669
r_dihedral_angle_3_deg	12.825
r_sphericity_bonded	6.838
r_dihedral_angle_1_deg	5.996
r_long_range_B_other	2.913
r_long_range_B_refined	2.912
r_rigid_bond_restr	2.785
r_mcangle_it	2.282
r_mcangle_other	2.282
r_scangle_other	2.233
r_scbond_other	1.935
r_scbond_it	1.934
r_mcbond_it	1.87
r_mcbond_other	1.87
r_angle_refined_deg	1.357
r_angle_other_deg	0.915
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_bond_other_d	0.007
r_gen_planes_refined	0.007
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	6664
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing