3AWO

Crystal structure of D-serine dehydratase in complex with D-serine from chicken kidney (EDTA-treated)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP, MICRO-SEEDING	6.5	293	12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, MICRO-SEEDING, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.053	α = 90
b = 105.053	β = 90
c = 81.916	γ = 90

Symmetry
Space Group	P 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	95	CCD	ADSC QUANTUM 270		2011-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A

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	2.65	100	99.9			13865	13850

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.79	99.9			7.04	1924

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.65	20	13118	13118	690	100	0.20928	0.20928	0.20623	0.26607	RANDOM	25.87

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]
-0.89			-0.89		1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.812
r_dihedral_angle_4_deg	18.41
r_dihedral_angle_3_deg	17.614
r_dihedral_angle_1_deg	5.839
r_scangle_it	2.298
r_scbond_it	1.345
r_angle_refined_deg	1.288
r_mcangle_it	1.075
r_mcbond_it	0.573
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.812
r_dihedral_angle_4_deg	18.41
r_dihedral_angle_3_deg	17.614
r_dihedral_angle_1_deg	5.839
r_scangle_it	2.298
r_scbond_it	1.345
r_angle_refined_deg	1.288
r_mcangle_it	1.075
r_mcbond_it	0.573
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2772
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	22

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.