7JZ9

Dihydrodipicolinate synthase S48F with pyruvate and succinic semi-aldehyde

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294.15	glucopyranoside, potassium phosphate dibasic

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.919	α = 90
b = 120.919	β = 90
c = 110.081	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	294.15	CCD	ADSC QUANTUM 315r		2011-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95369	Australian Synchrotron	MX2

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	1.82	33.34	100	0.086	17.5	11		83589

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.86			0.329	0.156

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YXC	1.82	33.27	78999	4156	99.96	0.14457	0.14318	0.17075	RANDOM	19.835

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.443
r_dihedral_angle_4_deg	18.446
r_dihedral_angle_3_deg	13.147
r_dihedral_angle_1_deg	6.328
r_long_range_B_other	5.947
r_long_range_B_refined	5.946
r_scangle_other	4.461
r_scbond_it	3.173
r_scbond_other	3.128
r_mcangle_other	2.609
r_mcangle_it	2.603
r_angle_refined_deg	2.218
r_mcbond_it	2.059
r_mcbond_other	2.05
r_angle_other_deg	1.206
r_chiral_restr	0.152
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4319
Nucleic Acid Atoms
Solvent Atoms	649
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing