2YXD

Crystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	OIL BATCH	6	298	50% PEG 400, 0.1M MES, pH 6.0, OIL BATCH, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.442	α = 90
b = 93.442	β = 90
c = 81.042	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	RIGAKU JUPITER 210			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	0.97891, 0.90000, 0.97928	SPring-8	BL26B1

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	2.3	50	98.9	0.089		12.6	16507	16322		-3

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	2.3	2.38	94.4		0.36		9.6	1539

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.3	20	14721	788	94.23	0.20171	0.19793	0.27322	RANDOM	49.032

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]
1.8			1.8		-3.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.42
r_dihedral_angle_3_deg	18.858
r_dihedral_angle_4_deg	15.103
r_dihedral_angle_1_deg	7.252
r_scangle_it	6.376
r_scbond_it	4.139
r_angle_refined_deg	2.486
r_mcangle_it	2.455
r_mcbond_it	1.553
r_nbtor_refined	0.333

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.42
r_dihedral_angle_3_deg	18.858
r_dihedral_angle_4_deg	15.103
r_dihedral_angle_1_deg	7.252
r_scangle_it	6.376
r_scbond_it	4.139
r_angle_refined_deg	2.486
r_mcangle_it	2.455
r_mcbond_it	1.553
r_nbtor_refined	0.333
r_symmetry_vdw_refined	0.32
r_nbd_refined	0.27
r_chiral_restr	0.195
r_xyhbond_nbd_refined	0.193
r_symmetry_hbond_refined	0.175
r_bond_refined_d	0.031
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2763
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.