2GKE | pdb_00002gke

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP

X-RAY DIFFRACTION

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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
2.48	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.394	α = 90
b = 104.02	β = 90
c = 59.936	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		2005-05-25	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	1.35	30	95.17			63225	63225

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	1.35	1.4	86.4

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	1.35	30	63225	63225	3204	95.17	0.13906	0.13906	0.13753	0.1455	0.16831	0.1712	RANDOM	10.417

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]
-0.62			0.29		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.399
r_dihedral_angle_4_deg	11.819
r_dihedral_angle_3_deg	10.45
r_dihedral_angle_1_deg	6.62
r_sphericity_free	5.854
r_scangle_it	4.717
r_scbond_it	3.446
r_rigid_bond_restr	3.163
r_sphericity_bonded	2.786
r_mcangle_it	2.266
r_mcbond_it	1.898
r_angle_refined_deg	1.508
r_angle_other_deg	0.714
r_mcbond_other	0.708
r_symmetry_vdw_refined	0.259
r_symmetry_vdw_other	0.238
r_symmetry_hbond_refined	0.223
r_xyhbond_nbd_refined	0.217
r_nbd_refined	0.205
r_nbd_other	0.201
r_nbtor_refined	0.177
r_chiral_restr	0.089
r_nbtor_other	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2122
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	32

Software

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