Experiment: 3GQX

Pyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crystal form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GQU	PDB ENTRY 3GQU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	290	500MM POTASSIUM IODIDE, 2% PEG 3350, pH 6.8, vapor diffusion, hanging drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
4.55	69.87
4	69.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.604	α = 90
b = 73.604	β = 90
c = 114.279	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93.15	IMAGE PLATE	RIGAKU RAXIS IV		2006-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.502

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.957	23.682	84	0.168		11.7		20529	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3GQU	2.5	23.682	0.03	19699	19699	1107	93.48	0.254	0.252	0.2538	0.287	0.2797	RANDOM	67.91

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]
-7.316			-7.316		14.631

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.045
f_angle_d	0.865
f_chiral_restr	0.072
f_bond_d	0.004
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1588
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	3

Software

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