Experiment: 2YQ8

Crystal structure of the SeMet-labeled N-terminal domain and peptide substrate binding domain of alpha subunit of prolyl-4 hydroxylase type I from human.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5F	PDB ENTRY 2V5F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		26-29% PEGMME 2000, 200MM KSCN AND 5MM DTT, 5MM SPERMINE TETRAHYDROCHLORIDE, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.4	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.878	α = 90
b = 72.017	β = 91.67
c = 66.431	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 315r		2011-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.99	45	96.7	0.08	13.23	3.4		19064		2.9	52.28

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	2.99	3.07	73.9		0.33	2.9	2.2

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 2V5F	2.987	44.622	1.37	19054	954	96.72	0.2124	0.2089	0.2107	0.2774	0.2792	45.9

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.276
f_angle_d	1.502
f_chiral_restr	0.088
f_bond_d	0.012
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3652
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Auto-Rickshaw	phasing