3VSD | pdb_00003vsd

Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	296	0.1M HEPES sodium pH 6.8, 27% 2-propanol, 10% PEG 4000, 5mM O-acetyl-L-serine, 5mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.646	α = 90
b = 75.646	β = 90
c = 275.784	γ = 90

Symmetry
Space Group	P 43 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	Bruker DIP-6040	rhodium-coated mirror (horizontal)	2009-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.09	50	97.7	0.08	10.7	7.8		47287			24.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.14	95.1		0.335		3.8	2232

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	FOURIER SYNTHESIS	THROUGHOUT	2.09	50	47256	2386	97.66	0.2367	0.2333	0.2344	0.3047	0.3073	RANDOM	44.646

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]
2.43			2.43		-4.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.869
r_dihedral_angle_4_deg	21.728
r_dihedral_angle_3_deg	19.433
r_dihedral_angle_1_deg	7.337
r_scangle_it	4.131
r_scbond_it	2.646
r_angle_refined_deg	1.867
r_mcangle_it	1.661
r_mcbond_it	0.942
r_chiral_restr	0.125

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.869
r_dihedral_angle_4_deg	21.728
r_dihedral_angle_3_deg	19.433
r_dihedral_angle_1_deg	7.337
r_scangle_it	4.131
r_scbond_it	2.646
r_angle_refined_deg	1.867
r_mcangle_it	1.661
r_mcbond_it	0.942
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5826
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	58

Software

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