5NFJ

Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	Well solution: 12% PEG 1000, 28% glycerol, 1.5%(w/v) PEG 3350 Cryo: 25% propylene glycol Protein concentration: 11 mg/mL

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.64	α = 90
b = 82.64	β = 90
c = 148.62	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2015-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92820	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.96	82.64	99.98	0.052	0.999	16.95	6.9		67692

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.96	82.64	67692	3570	99.98	0.18649	0.18533	0.20648	RANDOM	53.966

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]
1.37			1.37		-2.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.296
r_dihedral_angle_4_deg	17.549
r_dihedral_angle_3_deg	13.894
r_long_range_B_other	9.916
r_long_range_B_refined	9.914
r_scangle_other	7.903
r_dihedral_angle_1_deg	6.993
r_mcangle_it	6.453
r_mcangle_other	6.452
r_scbond_it	5.495
r_scbond_other	5.495
r_mcbond_it	4.672
r_mcbond_other	4.671
r_angle_refined_deg	1.878
r_angle_other_deg	1.074
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4387
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	139

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	phasing