3HWX | pdb_00003hwx

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	12% PEG 8K, 10% glycerol, 1mM ThDP, 5mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.353	α = 75.99
b = 90.463	β = 83
c = 169.17	γ = 64.15

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 270	mirrors	2009-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1	1.0000	PAL/PLS	6C1

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	2.4	50	83.5	0.15	0.26	6.22	2.4	141599	114098			14.5

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)
1	2.4	2.44	48.1		0.15	0.26	1.8	1.5	4413

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2JLC	2.6	47.69	141599	114098	5978	83.51	0.19946	0.19667	0.2	0.25271	0.22	RANDOM	14.503

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]
-0.09	0.04	-0.02	-0.02	-0.01	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.259
r_dihedral_angle_4_deg	20.994
r_dihedral_angle_3_deg	19.38
r_dihedral_angle_1_deg	6.895
r_scangle_it	3.055
r_scbond_it	1.868
r_angle_refined_deg	1.764
r_mcangle_it	1.108
r_mcbond_it	0.59
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.259
r_dihedral_angle_4_deg	20.994
r_dihedral_angle_3_deg	19.38
r_dihedral_angle_1_deg	6.895
r_scangle_it	3.055
r_scbond_it	1.868
r_angle_refined_deg	1.764
r_mcangle_it	1.108
r_mcbond_it	0.59
r_chiral_restr	0.114
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34608
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	243

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.