3B4U | pdb_00003b4u

Crystal structure of dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M Mg formate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.116	α = 79.35
b = 49.442	β = 89.06
c = 69.084	γ = 83.94

Symmetry
Space Group	P 1

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 315	Mirrors	2006-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID

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	1.2	67.88	93.19	0.077	17.89	4.7	169533	157988		2	9.8

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	1.2	1.231	72.49		0.274	3	3	13239

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	SAD	THROUGHOUT	1.2	67.88	157988	157988	8360	93.19	0.12846	0.12846	0.12703	0.14	0.15559	0.16	RANDOM	9.78

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]
0.38	-0.22	0.04	0.05	-0.12	-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.509
r_dihedral_angle_4_deg	19.801
r_dihedral_angle_3_deg	10.685
r_dihedral_angle_1_deg	6.268
r_sphericity_free	5.969
r_scangle_it	3.508
r_sphericity_bonded	3.197
r_scbond_it	2.659
r_mcangle_it	1.891
r_mcbond_it	1.56
r_angle_refined_deg	1.484
r_rigid_bond_restr	1.307
r_angle_other_deg	0.941
r_mcbond_other	0.621
r_symmetry_vdw_other	0.323
r_nbd_refined	0.244
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.17
r_symmetry_vdw_refined	0.141
r_nbtor_other	0.086
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4297
Nucleic Acid Atoms
Solvent Atoms	1354
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing