Experiment: 3BK2

Crystal Structure Analysis of the RNase J/UMP complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BK1	PDB entry 3BK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	2-4% PEG 4K, 0.02M ammonium sulfate, 0.1M Na-MES, The RNase J/UMP complex was obtained by soaking of a native RNase J crystal in 100mM UMP, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.08	α = 90
b = 118	β = 90
c = 228.32	γ = 90

Symmetry
Space Group	F 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	93	CCD	ADSC QUANTUM 315r		2007-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.93	ESRF	ID29

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	2.1	50	97.5	0.072	14.5	4.9	38744	38615			23.2

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	2.1	2.2	94.4		0.431	3.97	4.9	4991

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BK1	2.1	50	38744	38615	3869	99.7	0.227	0.227	0.217	0.2175	0.236	0.2353	RANDOM	41.961

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]
14.357			-18.111		3.754

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.315
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4304
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	46

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing