2GKJ | pdb_00002gkj

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor DL-AZIDAP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.8 M sodium acetate and 0.1 M HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.519	α = 90
b = 104.089	β = 90
c = 59.994	γ = 90

Symmetry
Space Group	C 2 2 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 210		2005-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115869	ALS	8.3.1

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	1.7	30	99.2			33348	33348

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	98.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.7	30	33348	33348	1665	99.2	0.17601	0.17601	0.17425	0.1649	0.20983	0.1598	RANDOM	14.883

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]
-0.29			-0.01		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.642
r_dihedral_angle_4_deg	12.189
r_dihedral_angle_3_deg	10.841
r_dihedral_angle_1_deg	6.032
r_scangle_it	2.177
r_mcangle_it	1.719
r_scbond_it	1.392
r_angle_refined_deg	1.322
r_mcbond_it	1.176
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.642
r_dihedral_angle_4_deg	12.189
r_dihedral_angle_3_deg	10.841
r_dihedral_angle_1_deg	6.032
r_scangle_it	2.177
r_mcangle_it	1.719
r_scbond_it	1.392
r_angle_refined_deg	1.322
r_mcbond_it	1.176
r_nbtor_refined	0.318
r_chiral_restr	0.278
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.184
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2146
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
SCALEPACK	data scaling
MOLREP	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.