3VSC | pdb_00003vsc

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	296	0.1M HEPES sodium pH 7.5, 25% 2-propanol, 10% PEG 4000, 5mM O-phospho-L-serine, 5mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.676	α = 90
b = 74.676	β = 90
c = 276.115	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	ADSC QUANTUM 315	rhodium-coated mirrors (horizontal and vertical)	2009-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.90000	SPring-8	BL41XU

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	2.07	50	99.2	0.079	9.1	8		48366			26.9

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	2.07	2.14	96.8		0.334		6.3	4584

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	2.07	50	48295	2439	99.27	0.1716	0.1686	0.169	0.2273	0.2245	RANDOM	35.3454

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]
1.79			1.79		-3.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.736
r_dihedral_angle_4_deg	19.946
r_dihedral_angle_3_deg	17.612
r_dihedral_angle_1_deg	6.689
r_scangle_it	6.025
r_scbond_it	3.785
r_mcangle_it	2.335
r_angle_refined_deg	2.261
r_mcbond_it	1.332
r_chiral_restr	0.251

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.736
r_dihedral_angle_4_deg	19.946
r_dihedral_angle_3_deg	17.612
r_dihedral_angle_1_deg	6.689
r_scangle_it	6.025
r_scbond_it	3.785
r_mcangle_it	2.335
r_angle_refined_deg	2.261
r_mcbond_it	1.332
r_chiral_restr	0.251
r_bond_refined_d	0.026
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5826
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	60

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.