9FPC | pdb_00009fpc

Architectural insights into the corrin and metal binding sites of CobN cobaltochelatase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.2 M Lithium sulfate, 30% polyethylene glycol 4000 and 0.1M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.43	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.13	α = 90
b = 74.19	β = 90
c = 85.89	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		2013-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

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	1.93	25.93	98.2	0.046	16.4	3.8		111314

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	1.93	1.98	86		0.339	2.3	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.965	7.143	27509	1391	96.465	0.176	0.173	0.1856	0.2288	0.2364	27.408

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]
0.013			0.002		-0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.844
r_dihedral_angle_3_deg	12.958
r_dihedral_angle_2_deg	12.757
r_lrange_it	6.946
r_lrange_other	6.925
r_dihedral_angle_1_deg	6.645
r_scangle_it	6.096
r_scangle_other	6.094
r_scbond_it	4.21
r_scbond_other	4.209
r_mcangle_it	3.633
r_mcangle_other	3.632
r_mcbond_it	2.766
r_mcbond_other	2.763
r_angle_refined_deg	2.196
r_angle_other_deg	1.11
r_nbd_refined	0.19
r_nbtor_refined	0.157
r_symmetry_nbd_other	0.138
r_nbd_other	0.132
r_chiral_restr	0.127
r_xyhbond_nbd_refined	0.127
r_symmetry_nbd_refined	0.109
r_symmetry_xyhbond_nbd_refined	0.088
r_symmetry_nbtor_other	0.064
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2967
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
BUCCANEER	phasing