1PPY

Native precursor of pyruvoyl dependent Aspartate decarboxylase

X-RAY DIFFRACTION

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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	5.5	292	NH42SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.1	59.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.983	α = 90
b = 70.983	β = 90
c = 216.386	γ = 120

Symmetry
Space Group	P 61 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 RAXIS IV		1999-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5482

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	1.95	62.02	96.4	0.058	24.5	17.9		20348		2.5	24.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.01	89.3		0.29	3.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1aw8	1.95	62.02	24605	20348	1183	95.51	0.15941	0.15941	0.15762	0.19522	RANDOM	14.99

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]
0.9	0.45		0.9		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.474
r_scangle_it	2.897
r_scbond_it	1.822
r_angle_refined_deg	1.425
r_mcangle_it	1.085
r_angle_other_deg	0.817
r_mcbond_it	0.652
r_symmetry_vdw_other	0.343
r_symmetry_hbond_refined	0.298
r_nbd_other	0.253
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.192
r_nbtor_other	0.114
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1755
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	5

Software

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