3RBL | pdb_00003rbl

Crystal structure of Human aromatic L-amino acid decarboxylase (AADC) in the apo form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RBF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapor diffusion followed by soaking	7	294	crystals obtained from holoAADC in 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0 were transferred in a ML droplet to yield apoAADC, vapor diffusion followed by soaking, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.64	α = 90
b = 179.64	β = 90
c = 74.95	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	ADSC QUANTUM 210		2010-11-20	M	SINGLE WAVELENGTH
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1
10	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.24	127.025	99.8	0.131	13.8	6.4	20098	20098

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.24	3.41	100		0.402	0.402	1.9	6.2	2886

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3rbf	3.24	30	20120	19980	1019	99.39	0.239	0.239	0.2361	0.24	0.2943	0.29	RANDOM	46.6904

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]
1.87			1.87		-3.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.851
r_dihedral_angle_3_deg	19.478
r_dihedral_angle_4_deg	18.835
r_dihedral_angle_1_deg	5.961
r_scangle_it	2.396
r_scbond_it	1.353
r_angle_refined_deg	1.271
r_mcangle_it	0.919
r_mcbond_it	0.464
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.851
r_dihedral_angle_3_deg	19.478
r_dihedral_angle_4_deg	18.835
r_dihedral_angle_1_deg	5.961
r_scangle_it	2.396
r_scbond_it	1.353
r_angle_refined_deg	1.271
r_mcangle_it	0.919
r_mcbond_it	0.464
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6949
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
EDNA	data collection

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.