4R3I | pdb_00004r3i

The crystal structure of an RNA complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		a different crystal form of same protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	291	25% PEG3350, 0.2 M amonium sulfate, 0.1 M bis-tris, pH 6.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.728	α = 90
b = 39.748	β = 103.56
c = 56.238	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	IMAGE PLATE	RIGAKU RAXIS		2014-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.8	34.73	97.1	0.112	8.5	3.6		14029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	90.7		0.587	0.369	2.3	3.3	773

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	a different crystal form of same protein	1.8	30	14013	700	97.17	0.2064	0.2034	0.21	0.2636	0.27	RANDOM	21.3503

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]
-1.33		0.74	-1.57		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.952
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_3_deg	11.705
r_dihedral_angle_1_deg	6.206
r_mcangle_it	2.749
r_mcbond_it	1.826
r_mcbond_other	1.825
r_angle_refined_deg	1.371
r_angle_other_deg	0.792
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1275
Nucleic Acid Atoms	106
Solvent Atoms	89
Heterogen Atoms	7

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction