5C5U | pdb_00005c5u

The crystal structure of viral collagen prolyl hydroxylase vCPH from Paramecium Bursaria Chlorella virus-1 - Truncated Construct

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	vCPH was concentrated to 30 mg/ml in 100 mM HEPES, pH 7.5, before being supplemented with 1.1 mM MnCl2. Crystals of vCPH were grown by sitting drop vapour diffusion, incubated at 4 C and arose from a reservoir solution containing 0.1 M [Imidazole; MES monohydrate (acid)], 0.1 M amino acids [0.2 M L-Na-Glutamate; 0.2 M Alanine (racemic); 0.2 M Glycine; 0.2M Lysine HCL (racemic); 0.2 M Serine (racemic)], 30 % PEGMME 550 PEG 20K pH 6.5 [Morpheus HT96 condition H1, Molecular Dimensions].

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.77	α = 90
b = 157.67	β = 90.02
c = 41.01	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M		2012-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	28.4	94.56	10.4	3.1		44328

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	FREE R-VALUE	2JIG	1.7	28.4	2.02	44328	2085	94.56	0.163	0.156	0.16	0.2024	0.21

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	12.698
f_angle_d	0.872
f_chiral_restr	0.044
f_bond_d	0.005
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms
Solvent Atoms	526
Heterogen Atoms	17

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	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.