3OKC | pdb_00003okc

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OKA	PDB entry 3oka

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.1	291	0.1 M sodium citrate pH 5.1, 22% PEG 3350 , VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.852	α = 90
b = 86.4	β = 90
c = 106.639	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 4		2010-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	2.23	45.37	95.8	0.093	0.093	9.9	3.2	19982	19982			28

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)
	2.23	2.35	72.5		0.382	0.382	2.3	2.3	4871

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3oka	2.4	45.36	15991	15991	851	99.69	0.19245	0.19245	0.19009	0.19	0.23617	0.24	RANDOM	20.345

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]
-0.76			0.14		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.386
r_dihedral_angle_3_deg	13.874
r_dihedral_angle_4_deg	13.711
r_dihedral_angle_1_deg	4.957
r_scangle_it	1.472
r_angle_refined_deg	1.09
r_scbond_it	0.842
r_mcangle_it	0.547
r_mcbond_it	0.339
r_nbtor_refined	0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.386
r_dihedral_angle_3_deg	13.874
r_dihedral_angle_4_deg	13.711
r_dihedral_angle_1_deg	4.957
r_scangle_it	1.472
r_angle_refined_deg	1.09
r_scbond_it	0.842
r_mcangle_it	0.547
r_mcbond_it	0.339
r_nbtor_refined	0.291
r_symmetry_vdw_refined	0.194
r_nbd_refined	0.171
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.068
r_symmetry_hbond_refined	0.038
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2850
Nucleic Acid Atoms
Solvent Atoms	140
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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.