2NZ4

Structural investigation of the GlmS ribozyme bound to its catalytic cofactor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	298	11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.127	α = 90
b = 234.157	β = 90.65
c = 105.003	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	CCD	ADSC QUANTUM 315		2006-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.498	34.94	99.8	0.062	0.046	23.2	6.1		79785		1.1	87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.498	2.59	100		1.1	5.9	7928

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MIR	THROUGHOUT	2.498	34.94	2.2	75624	3987	99.35	0.22395	0.22157	0.26	0.26897	0.3	RANDOM	50.64

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]
0.2		-0.26	-0.02		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.13
r_dihedral_angle_3_deg	16.817
r_dihedral_angle_4_deg	15.145
r_dihedral_angle_1_deg	6.947
r_mcangle_it	1.837
r_angle_refined_deg	1.507
r_scangle_it	1.233
r_mcbond_it	1.201
r_angle_other_deg	0.972
r_scbond_it	0.816
r_mcbond_other	0.326
r_symmetry_hbond_refined	0.242
r_nbtor_refined	0.224
r_nbd_other	0.219
r_xyhbond_nbd_refined	0.196
r_symmetry_vdw_other	0.189
r_nbd_refined	0.154
r_symmetry_vdw_refined	0.144
r_metal_ion_refined	0.12
r_nbtor_other	0.082
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2908
Nucleic Acid Atoms	13080
Solvent Atoms	206
Heterogen Atoms	80

Software

Software
Software Name	Purpose
CBASS	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling