6M1X | pdb_00006m1x

Crystal structure of Phosphoserine Phosphatase in complex with 3-Phosphoglyceric Acid from Entamoeba histolytica

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZKK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.1 M MMT buffer pH-4.0, PEG-1500 (20%), 0.2 M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.976	α = 90
b = 112.388	β = 90
c = 177.428	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	82	IMAGE PLATE	RIGAKU RAXIS IV++		2016-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.48	88.87	96.1	1	10.83	4.1		33163

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	2.48	2.59			0.506	0.843

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 (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	FREE R-VALUE	5ZKK	2.48	88.87	31433	1718	95.2	0.2299	0.2284	0.24	0.2564	0.26	RANDOM	54.274

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]
-1.98			-4.44		6.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.571
r_dihedral_angle_3_deg	17.858
r_dihedral_angle_4_deg	13.906
r_dihedral_angle_1_deg	5.947
r_angle_refined_deg	1.619
r_angle_other_deg	1.027
r_chiral_restr	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.571
r_dihedral_angle_3_deg	17.858
r_dihedral_angle_4_deg	13.906
r_dihedral_angle_1_deg	5.947
r_angle_refined_deg	1.619
r_angle_other_deg	1.027
r_chiral_restr	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5895
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	32

Software

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