5AES | pdb_00005aes

Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with a PNP-derived Inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BX3	PDB ENTRY 4BX3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		0.1M IMIDAZOLE (PH 8.0), 0.2M NACL, 1M SODIUM TARTRATE

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.81	α = 90
b = 166.81	β = 90
c = 166.81	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS	2013-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	2.75	32.71	100	0.1	13	7.3		20219		-3	67.02

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	2.75	2.9	100		0.95	1.9	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 4BX3	2.751	32.714	1.34	20098	1026	99.46	0.1923	0.1895	0.2	0.2466	0.24	50.8

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]
3.3788	-0.4678	-1.0621	0.4361	0.3969	0.124

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.179
f_angle_d	0.932
f_chiral_restr	0.044
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4403
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	40

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	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.