3SS7 | pdb_00003ss7

Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.7 M sodium citrate, 0.1 M imidazole/maleate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.774	α = 90
b = 47.806	β = 104.96
c = 75.193	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.979	SRS	PX10.1

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	1.55	72.74		0.085	15.9	4.7		73947		2	15.8

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	1.55	1.61			0.41	2.25	2.5

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	1.55	50	70687	3546	95.59	0.161	0.1592	0.1569	0.1939	0.1915	RANDOM	16.9927

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]
-0.36		0.19	0.25		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.805
r_dihedral_angle_4_deg	14.08
r_dihedral_angle_3_deg	12.761
r_dihedral_angle_1_deg	5.351
r_scangle_it	3.765
r_scbond_it	2.466
r_angle_refined_deg	1.524
r_mcangle_it	1.503
r_mcbond_it	0.9
r_metal_ion_refined	0.378

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.805
r_dihedral_angle_4_deg	14.08
r_dihedral_angle_3_deg	12.761
r_dihedral_angle_1_deg	5.351
r_scangle_it	3.765
r_scbond_it	2.466
r_angle_refined_deg	1.524
r_mcangle_it	1.503
r_mcbond_it	0.9
r_metal_ion_refined	0.378
r_nbtor_refined	0.313
r_nbd_refined	0.24
r_symmetry_vdw_refined	0.218
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3324
Nucleic Acid Atoms
Solvent Atoms	668
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.