3LQS | pdb_00003lqs

Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Crystals were grown by the hanging drop method . The enzyme was dialyzed in 0.2 M potassium phosphate buffer pH 7.2, concentrated to 40mg/mL, and incubated with an R-ADTA:protein molecular ratio of 200:1 prior to crystallization. The enzyme solution was mixed with crystallization buffer at pH 8.5 and incubated initially at 30-40 C, then allowed to return to room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.011	α = 90
b = 90.728	β = 90
c = 88.893	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	63.5	97.4	14.9	4		48439

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	1.97	95		0.509	2.5		4660

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	63.5	45930	2465	97.29	0.16234	0.16052	0.16	0.19585	0.19	RANDOM	23.108

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]
0.08			1.02		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.436
r_dihedral_angle_3_deg	15.003
r_dihedral_angle_4_deg	14.494
r_dihedral_angle_1_deg	5.33
r_scangle_it	4.277
r_scbond_it	2.71
r_angle_refined_deg	1.764
r_mcangle_it	1.649
r_mcbond_it	1.009
r_symmetry_vdw_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.436
r_dihedral_angle_3_deg	15.003
r_dihedral_angle_4_deg	14.494
r_dihedral_angle_1_deg	5.33
r_scangle_it	4.277
r_scbond_it	2.71
r_angle_refined_deg	1.764
r_mcangle_it	1.649
r_mcbond_it	1.009
r_symmetry_vdw_refined	0.323
r_nbtor_refined	0.307
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.198
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4514
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.