5E3R | pdb_00005e3r

Crystal structure of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E3P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 200, MgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.446	α = 90
b = 92.446	β = 90
c = 279.602	γ = 120

Symmetry
Space Group	H 3 2

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		2015-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	93.2	97.8	32.36	5.1		36690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	97.8		4.15	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	5E3P	1.85	93.2	36690	2007	97.8	0.179	0.1776	0.19	0.2057	0.22	RANDOM	28.762

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]
0.9	0.45		0.9		-2.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.526
r_dihedral_angle_4_deg	22.523
r_dihedral_angle_3_deg	12.787
r_dihedral_angle_1_deg	6.889
r_mcangle_it	3.836
r_mcbond_it	2.985
r_mcbond_other	2.912
r_angle_refined_deg	2.132
r_angle_other_deg	1.117
r_chiral_restr	0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.526
r_dihedral_angle_4_deg	22.523
r_dihedral_angle_3_deg	12.787
r_dihedral_angle_1_deg	6.889
r_mcangle_it	3.836
r_mcbond_it	2.985
r_mcbond_other	2.912
r_angle_refined_deg	2.132
r_angle_other_deg	1.117
r_chiral_restr	0.154
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2046
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	12

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

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.