Experiment: 3FHY

Crystal structure of D235N mutant of human pyridoxal kinase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YXU	PDB entry 2YXU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Protein solution: 20 mM Sodium BES buffer pH 7.2, 100 mM NaCl, 5 mM BME, 2.5 mM MgATP. Precipitant: 100 mM Tris-HCl pH 8.0, 57%, MPD, 5 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.11	α = 90
b = 114.643	β = 90
c = 169.681	γ = 90

Symmetry
Space Group	I 2 2 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	IMAGE PLATE	RIGAKU RAXIS IV	MSC Varimax confocal optics	2008-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

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	2.3	32.54	99	0.049		3.39		39415

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)
	2.3	2.38	99.3		0.25	4.6	3.18	3924

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 2YXU	2.3	29.36	39410	39410	1954	98.8	0.219	0.219	0.214	0.2047	0.261	0.2015	RANDOM	45.209

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]
16.26			-8.17		-8.09

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.9
c_scangle_it	10.71
c_scbond_it	9.4
c_mcangle_it	7.77
c_mcbond_it	6.19
c_angle_deg	1.4
c_improper_angle_d	0.95
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4828
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	126

Software

Software
Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing