2A6N | pdb_00002a6n

Dihydrodipicolinate synthase (E. coli)- mutant R138A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	284	protein solution (~5 mg/ml in Tris.HCl 20 mM, pH 8, 2.5 uL), precipitant (K2HPO4 1.8 M, pH 10, 1.2 uL), and N-octyl- -R-glucopyranoside (6% w/v, 0.6 uL), VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.989	α = 90
b = 120.989	β = 90
c = 111.302	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.8	39.6	100	0.063		5.63	87227	87227

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)
	1.8	1.86	100		0.394	4	5.43

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 (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	1.94	33.33	66352	66352	3515	100	0.16421	0.16281	0.17	0.19142	0.2	RANDOM	20.637

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]
-0.24	-0.12		-0.24		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.142
r_dihedral_angle_4_deg	15.901
r_dihedral_angle_3_deg	13.557
r_dihedral_angle_1_deg	6.188
r_scangle_it	3.483
r_scbond_it	2.152
r_angle_refined_deg	1.339
r_mcangle_it	1.209
r_angle_other_deg	0.852
r_mcbond_it	0.632
r_symmetry_vdw_other	0.274
r_nbd_refined	0.23
r_nbd_other	0.181
r_symmetry_vdw_refined	0.17
r_nbtor_refined	0.165
r_mcbond_other	0.15
r_xyhbond_nbd_refined	0.137
r_metal_ion_refined	0.13
r_nbtor_other	0.087
r_symmetry_hbond_refined	0.086
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
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	4301
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
AMoRE	phasing