3OKA

Crystal structure of Corynebacterium glutamicum PimB' in complex with GDP-Man (triclinic crystal form)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	6-26% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.1 M lithium sulfate and 0.1 M glycine, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.07	α = 92.05
b = 50.02	β = 92.68
c = 85.3	γ = 89.94

Symmetry
Space Group	P 1

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		2008-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9762	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	43.8	95.1	0.073	0.073	11.6	2.9	35191	35191			17.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.32	81.2		0.238	0.238	5.9	2.8	4400

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	2.2	43.8	33243	33243	1747	94.81	0.19097	0.19097	0.18937	0.221	RANDOM	13.213

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	-0.23	-0.14	-0.94	0.09	0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.537
r_dihedral_angle_4_deg	16.682
r_dihedral_angle_3_deg	13.186
r_dihedral_angle_1_deg	5.219
r_scangle_it	1.961
r_scbond_it	1.167
r_angle_refined_deg	1.15
r_mcangle_it	0.691
r_mcbond_it	0.408
r_nbtor_refined	0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.537
r_dihedral_angle_4_deg	16.682
r_dihedral_angle_3_deg	13.186
r_dihedral_angle_1_deg	5.219
r_scangle_it	1.961
r_scbond_it	1.167
r_angle_refined_deg	1.15
r_mcangle_it	0.691
r_mcbond_it	0.408
r_nbtor_refined	0.295
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.186
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.081
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5825
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	112

Software

Software
Software Name	Purpose
ADSC	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.