4KO2 | pdb_00004ko2

Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KL8	PDB entry 4KL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.23	α = 90
b = 108.91	β = 90
c = 136.34	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	CCD	ADSC QUANTUM 315r		2010-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.1399	ESRF	ID14-4

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	1.6	30	93.1	0.157	8	6.8	207784	193492			22.1

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	1.6	1.7	66.6		1.763	0.58	4.5	34201

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 (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	PDB entry 4KL8	1.6	25	207754	183664	9799	93.35	0.16386	0.16225	0.163	0.194	0.1943	RANDOM	17.57

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]
-0.04			-0.56		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.181
r_dihedral_angle_4_deg	17.2
r_dihedral_angle_3_deg	11.478
r_scangle_it	5.87
r_dihedral_angle_1_deg	5.523
r_scbond_it	4.127
r_mcangle_it	2.904
r_rigid_bond_restr	2.216
r_mcbond_it	1.933
r_angle_refined_deg	1.27
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11946
Nucleic Acid Atoms
Solvent Atoms	1780
Heterogen Atoms	98

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction