2ANN | pdb_00002ann

Crystal structure (I) of Nova-1 KH1/KH2 domain tandem with 25 nt RNA hairpin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EC6	Nova-2 KH3 domain from PDB ENTRY 1EC6, and idealised 5 bp A-RNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	293	PEG 4000, isopropanole, sodium citrate, potassium chloride, magnesium chloride, pH 5.6, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.304	α = 90
b = 37.147	β = 94.42
c = 34.825	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	APS-1		2002-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0080	APS	19-ID

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	2.3	50	99.7	0.068		3.5		9118

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	2.3	2.38	97.9	97.9	0.444

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Nova-2 KH3 domain from PDB ENTRY 1EC6, and idealised 5 bp A-RNA	2.3	20	9010	8981	430	99.77	0.196	0.196	0.193	0.249	0.2826	RANDOM	27.912

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]
-0.33		-1.13	2.02		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.644
r_scangle_it	2.617
r_scbond_it	1.728
r_angle_refined_deg	1.335
r_mcangle_it	1.129
r_mcbond_it	0.592
r_metal_ion_refined	0.27
r_symmetry_hbond_refined	0.253
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1118
Nucleic Acid Atoms	491
Solvent Atoms	77
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data scaling
AMoRE	phasing