Experiment: 4CUG

Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.1M TRIS-HCL PH8.5, 1MM MNCL2, 1MM OGA, 2MM L16 PEPTIDE, 0.66MM PROTEIN, 0.1M AMMONIUM DIHYDROGEN PHOSPHATE, 45% (V/V) METHYL-2-4-PENTANEDIOL, ROOM TEMPERATURE

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 117.47	β = 90
c = 120.28	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M	MIRRORS	2012-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.96	58.74	99.9	0.05	19.4	6.4		29641		-3	97.22

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	2.96	3.04	100		0.77	2.6	6.3

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 4CCL	2.96	58.74	1.49	29585	2001	99.86	0.2112	0.2101	0.2198	0.227	0.2369	106.55

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	14.753
f_angle_d	0.775
f_chiral_restr	0.031
f_plane_restr	0.005
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6219
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	43

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing