7A8Y

X-ray crystal structure of Aspartate alpha-decarboxylase in complex with D-Serine

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	293	1.8 M ammonium sulphate, 100 mM sodium citrate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.3	α = 90
b = 71.3	β = 90
c = 216.65	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	PIXEL	DECTRIS PILATUS 6M		2010-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9778	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.75	46.98	99.99	0.02384	0.99	21.5	2		33922

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81			0.1564	0.93	5.25

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1AW8	1.75	46.975	33922	1702	99.988	0.171	0.1705	0.1905	20.673

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]
0.257	0.129		0.257		-0.835

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.113
r_dihedral_angle_1_deg	16.825
r_dihedral_angle_3_deg	14.106
r_dihedral_angle_4_deg	9.698
r_lrange_it	5.322
r_lrange_other	5.321
r_scangle_it	2.158
r_scangle_other	2.157
r_mcangle_it	1.939
r_mcangle_other	1.939
r_scbond_it	1.317
r_scbond_other	1.317
r_angle_refined_deg	1.258
r_angle_other_deg	1.244
r_mcbond_it	1.111
r_mcbond_other	1.111
r_nbd_other	0.246
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.208
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_other	0.158
r_symmetry_xyhbond_nbd_refined	0.151
r_nbtor_refined	0.148
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.053
r_bond_refined_d	0.004
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1828
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	40

Software

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