5HUD | pdb_00005hud

Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2W1A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro-seeded from badly diffracting crystals (approx. 8 AA resolution), in 100 mM Na-HEPES, pH 7.5, 200 mM LiSO4, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.622	α = 90
b = 110.481	β = 101.41
c = 134.652	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2015-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97239	ESRF	ID29

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	2.1	131.99	96.7	0.199	4.79	2.95		190339

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	2.1	2.23	85.7		1.763	0.44	2.24

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	2W1A	2.15	40	170847	8846	97.99	0.25191	0.24952	0.25	0.298	0.3	RANDOM	33.789

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]
0.57		0.09	-1.03		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.924
r_dihedral_angle_3_deg	16.337
r_dihedral_angle_4_deg	16.187
r_dihedral_angle_1_deg	6.091
r_long_range_B_refined	5.8
r_long_range_B_other	5.8
r_scangle_other	3.552
r_mcangle_it	3.154
r_mcangle_other	3.154
r_scbond_it	2.165
r_scbond_other	2.165
r_mcbond_it	1.926
r_mcbond_other	1.926
r_angle_refined_deg	1.531
r_angle_other_deg	0.986
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
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	16558
Nucleic Acid Atoms
Solvent Atoms	779
Heterogen Atoms	871

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
XDS	data scaling
XDS	data reduction