3OKP

Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic crystal form)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.1	291	0.1 M DL-malic acid pH 6.1, 13% PEG 3350 , VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.746	α = 90
b = 87.002	β = 90
c = 106.895	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		2010-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	Diamond	I04

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	37.29	100	0.096	0.096	18.3	7.2	28997	28997			15.9

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	2.11	99.8		0.38	0.38	5.7	7.2	4147

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3oka	2	37.29	27519	27519	1476	99.93	0.20408	0.20256	0.2321	RANDOM	14.231

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]
-0.21			0.05		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.301
r_dihedral_angle_3_deg	12.804
r_dihedral_angle_4_deg	11.101
r_dihedral_angle_1_deg	4.856
r_scangle_it	1.076
r_angle_refined_deg	1.022
r_scbond_it	0.65
r_mcangle_it	0.432
r_nbtor_refined	0.292
r_mcbond_it	0.259

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.301
r_dihedral_angle_3_deg	12.804
r_dihedral_angle_4_deg	11.101
r_dihedral_angle_1_deg	4.856
r_scangle_it	1.076
r_angle_refined_deg	1.022
r_scbond_it	0.65
r_mcangle_it	0.432
r_nbtor_refined	0.292
r_mcbond_it	0.259
r_nbd_refined	0.17
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.091
r_symmetry_hbond_refined	0.066
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2827
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	28

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	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.