3SPA | pdb_00003spa

Crystal Structure of Human Mitochondrial RNA Polymerase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QLN	PDB entry 1QLN, truncated to polyAlanine, residues 246-354, 392-568, 691-741, 766-883 of model used

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	12% PEG4000, 10% Glycerol, 30mM Mes 6.5, 60mM (NH4)2SO4, 40mM Tris 8.0, 20mM DTT in situ proteolysed with ArgC (1:1000 w/w ratio) and micro-seeded, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.258	α = 90
b = 211.258	β = 90
c = 60.461	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	63	CCD	MARMOSAIC 225 mm CCD		2011-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

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	2.5	58.128		0.047	15.9	3.8	46595	46507			73.16

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	2.5	2.64			0.631	1.9	3.8	6694

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 1QLN, truncated to polyAlanine, residues 246-354, 392-568, 691-741, 766-883 of model used	2.5	58.128	46507	46505	2378	99.81	0.1878	0.1878	0.1855	0.2135	0.231	0.2484	RANDOM	89.21

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]
9.3566			9.3566		-18.7131

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	19.41
t_omega_torsion	2.6
o_angle_deg	1.12
o_bond_d	0.009
o_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7457
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	22

Software

Software
Software Name	Purpose
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling