4KO3 | pdb_00004ko3

Low X-ray dose structure of 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	46.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.2	α = 90
b = 108.72	β = 90
c = 136.62	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	1.7	30	99.1	0.177	6.3	6.5	173572	171915			21.7

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	1.7	1.8	94.1		1.349	0.65	3.4	27085

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	1.7	25	173542	163172	8712	99.05	0.16573	0.16385	0.1649	0.20071	0.201	RANDOM	14.582

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]
0.36			-0.48		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.421
r_dihedral_angle_4_deg	17.202
r_dihedral_angle_3_deg	11.691
r_dihedral_angle_1_deg	5.562
r_scangle_it	5.25
r_scbond_it	3.664
r_mcangle_it	2.522
r_rigid_bond_restr	1.938
r_mcbond_it	1.633
r_angle_refined_deg	1.252
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11944
Nucleic Acid Atoms
Solvent Atoms	1843
Heterogen Atoms	99

Software

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