4D7Z | pdb_00004d7z

E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AW8	PDB ENTRY 1AW8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8		ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 MM DTT. THIS WAS MIXED IN A 1:1 RATIO WITH RESERVOIR SOLUTION (0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS- TRIS PROPANE PH 6.8, 20 % W/V PEG 3350) AND CRYSTALLIZED BY HANGING DROP VAOUR DIFFUSION (4 UL DROPLET OVER A 1 ML RESERVOIR).

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.35	α = 90
b = 71.35	β = 90
c = 112.31	γ = 90

Symmetry
Space Group	I 4 2 2

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 IMAGE PLATE	VARIMAX	2014-09-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.9	23.26	99.9	0.14	9.9	6.4		11805			10.3

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	1.9	1.94	100		0.64	2.6	5.8

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 1AW8	1.9	60.22	11235	552	99.75	0.18894	0.18622	0.2	0.24418	0.26	RANDOM	24.788

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]
0.6			0.6		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.232
r_dihedral_angle_3_deg	14.51
r_dihedral_angle_4_deg	10.197
r_dihedral_angle_1_deg	6.636
r_scbond_it	3.244
r_mcangle_it	2.968
r_mcbond_it	2.039
r_mcbond_other	2.029
r_angle_refined_deg	1.737
r_angle_other_deg	0.826
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	942
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing