2XVY

Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hildenborough (co-crystallised with cobalt and SHC)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XVZ	PDB ENTRY 2XVZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0.2UL OF COBALT CHLORIDE IN AEROBIC CONDITIONS.

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.81	α = 90
b = 120.81	β = 90
c = 119.71	γ = 90

Symmetry
Space Group	I 4 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	100	CCD	MARRESEARCH	COLLIMATING RHODIUM COATED MIRROR (BEFORE MONOCHROMATOR) AND FOCUSSING TOROIDAL RHODIUM COATED MIRROR (AFTER MONOCHROMATOR)	2007-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	1.7	49.24	96.7	0.04	20.8	5.4		46830			30.5

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	1.7	1.81	84.4		0.46	2.9	4.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2XVZ	1.7	85.44	44493	2379	96.79	0.17296	0.17215	0.18779	RANDOM	25.875

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]
-0.43			-0.43		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.72
r_dihedral_angle_4_deg	18.116
r_dihedral_angle_3_deg	12.76
r_dihedral_angle_1_deg	5.026
r_scangle_it	4.83
r_scbond_it	3.036
r_mcangle_it	1.915
r_angle_refined_deg	1.762
r_mcbond_it	1.088
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1979
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	120

Software

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