5X7M | pdb_00005x7m

Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HKV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Sodium citrate tribasic, Sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.65	α = 90
b = 92.013	β = 90
c = 94.753	γ = 90

Symmetry
Space Group	P 21 21 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		2016-06-10	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	2.4	94.76	96	26.88	4.7		36222

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	2.4	2.44

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	1HKV	2.4	23.708	36222	1898	95.52	0.1897	0.1864	0.19	0.2531	0.26	RANDOM	35.912

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]
-0.63			0.76		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.499
r_dihedral_angle_4_deg	17.033
r_dihedral_angle_3_deg	15.097
r_dihedral_angle_1_deg	7.584
r_angle_refined_deg	1.725
r_angle_other_deg	1.025
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.499
r_dihedral_angle_4_deg	17.033
r_dihedral_angle_3_deg	15.097
r_dihedral_angle_1_deg	7.584
r_angle_refined_deg	1.725
r_angle_other_deg	1.025
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6652
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	30

Software

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

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.