1UWV | pdb_00001uwv

Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9		PROTEIN WAS CRYSTALLIZED FROM 50 MM TRIS-CL (PH 9-9.5), 10 MM NICL2, 12.5% GLYCEROL, AND 20% POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.938	α = 90
b = 99.448	β = 100.57
c = 58.519	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 CCD QUANTUM-4 2X2 ARRAY	MIRRORS	2002-02-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9786,0.9788	ALS	5.0.2

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	1.95	50	100	0.094	18.4	7.5		29176		2.6

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	1.95	1.98	100		0.896	2.6	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.95	50	27660	1477	99.6	0.186	0.227	RANDOM	17.1

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]
1.09		0.51	-1.6		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.389
r_scangle_it	5.155
r_scbond_it	3.506
r_mcangle_it	1.737
r_angle_refined_deg	1.673
r_mcbond_it	0.938
r_angle_other_deg	0.892
r_symmetry_vdw_other	0.306
r_symmetry_vdw_refined	0.267
r_nbd_other	0.247
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.194
r_symmetry_hbond_refined	0.188
r_chiral_restr	0.1
r_nbtor_other	0.087
r_metal_ion_refined	0.047
r_bond_refined_d	0.019
r_gen_planes_other	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3239
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	16

Software

Software
Software Name	Purpose
Quanta	model building
SCALEPACK	data scaling
CNS	phasing
CCP4	phasing
SHARP	phasing
Quanta	phasing
REFMAC	refinement