Experiment: 3HY8

Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NRG	PDB Entry 1NRG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	295	mono-ammonium dihydrogen phosphate, Sodium Citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.27	α = 90
b = 82.27	β = 90
c = 58.788	γ = 120

Symmetry
Space Group	P 31 2 1

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	mirrors	2008-10-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2.5	35.63	99.8	0.056	22.5	9.66		8215			62.1

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	2.5	2.59	100		0.33	6.5	9.79	800

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	FOURIER SYNTHESIS	THROUGHOUT	PDB Entry 1NRG	2.5	22.02	8195	8195	382	99.9	0.229	0.229	0.226	0.2252	0.287	0.29	RANDOM	61.287

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]
0.31	8.31		0.31		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_scangle_it	9.29
c_mcangle_it	7.38
c_scbond_it	7.3
c_mcbond_it	5.45
c_angle_deg	1.3
c_improper_angle_d	0.96
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1732
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	62

Software

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