6LVR

Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	1.5 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.48	α = 90
b = 131.701	β = 90
c = 155.556	γ = 90

Symmetry
Space Group	P 21 21 2

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 EIGER X 16M		2017-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.85	50	99.9	0.124	0.055	13.8	5		42492

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.9	100		1.075	0.48	0.792	1.56	4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4G24, 1EHZ	2.85	49.312	41250	2087	99.821	0.236	0.2347	0.2554	120.68

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]
0.223			-1.877		1.655

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.575
r_dihedral_angle_4_deg	25.43
r_dihedral_angle_3_deg	19.879
r_rigid_bond_restr	15.104
r_lrange_other	4.463
r_lrange_it	4.41
r_dihedral_angle_1_deg	4.302
r_scangle_it	3.068
r_scangle_other	3.067
r_angle_other_deg	2.249
r_scbond_other	2.081
r_mcangle_other	1.952
r_mcangle_it	1.918
r_scbond_it	1.818
r_angle_refined_deg	1.606
r_mcbond_other	1.192
r_mcbond_it	1.137
r_symmetry_xyhbond_nbd_refined	0.26
r_symmetry_nbd_other	0.257
r_nbd_other	0.232
r_nbtor_refined	0.209
r_xyhbond_nbd_refined	0.177
r_nbd_refined	0.175
r_symmetry_nbd_refined	0.15
r_chiral_restr	0.124
r_symmetry_xyhbond_nbd_other	0.105
r_symmetry_nbtor_other	0.08
r_bond_other_d	0.028
r_bond_refined_d	0.027
r_gen_planes_refined	0.023
r_gen_planes_other	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3055
Nucleic Acid Atoms	3136
Solvent Atoms	35
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing