2OTN | pdb_00002otn

Crystal structure of the catalytically active form of diaminopimelate epimerase from Bacillus anthracis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.6	293	0.2 M ammonium formate, 20% PEG 3350, 3% ethylene glycol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.60

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.863	α = 90
b = 87.334	β = 90
c = 110.453	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2005-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	98.9	0.074	23.6	6.7		24966		-4	54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			0.488	3.1

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	PDB ENTRY 1GQZ	2.4	36.23	23674	1234	98.9	0.184	0.18	0.18	0.25	0.25	RANDOM	25.879

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]
-1.67			0.51		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.73
r_dihedral_angle_3_deg	16.215
r_dihedral_angle_4_deg	14.402
r_scangle_it	6.75
r_dihedral_angle_1_deg	6.722
r_scbond_it	5.469
r_mcangle_it	4.193
r_mcbond_it	3.497
r_angle_refined_deg	1.329
r_angle_other_deg	1.145
r_mcbond_other	0.874
r_symmetry_vdw_other	0.241
r_symmetry_hbond_refined	0.209
r_nbd_other	0.198
r_nbd_refined	0.182
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.131
r_nbtor_other	0.086
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4470
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing