Experiment: 5LAT

HIF prolyl hydroxylase 2 (PHD2/EGLN1) P317R variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.1 M tri-sodium citrate pH 5.6, 20% PEG 4000, 20% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.182	α = 90
b = 111.182	β = 90
c = 40.028	γ = 120

Symmetry
Space Group	P 63

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	MIRRORS	2007-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	27.8	99.6	0.088	0.991	9.1	2.8		22463			21.36

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	1.9	2	99.8		0.354	2.9	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	THROUGHOUT	4BQX	1.9	27.796	1.35	22455	1149	99.49	0.1512	0.1504	0.1537	0.1659	0.1676	33

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]
-2.87			-2.87		5.75

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.477
f_angle_d	0.852
f_chiral_restr	0.052
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1718
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	30

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing