Experiment: 3DHS

Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A64	PDB entry 2a64

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	296	0.05 M cacodylate, 0.1 M potassium chloride, 0.02 M magnesium chloride, 0.001 M spermine tetrachloride, 23% 1,6-hexanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
4.52	72.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.35	α = 90
b = 160.01	β = 90
c = 133.45	γ = 90

Symmetry
Space Group	C 2 2 2

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	ADSC QUANTUM 210		2004-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.1401	ALS	8.2.1

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	3.6	42.07	98.7	0.102	10.2	13.64		18374

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)
	3.6	3.73	98.6		0.714	2.9	13.66	1786

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-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 2a64	3.6	42.07	18347	2357	97.1	0.29	0.3541	0.314	0.3758	RANDOM	209.908

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]
-40.84			2.13		38.71

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	14.1
c_improper_angle_d	1.42
c_angle_deg	0.8
c_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	4613
Solvent Atoms
Heterogen Atoms	15

Software

Software
Software Name	Purpose
d*TREK	data scaling
CNS	refinement
CNS	phasing
PDB_EXTRACT	data extraction
ADSC	data collection
d*TREK	data reduction