Experiment: 3PQ1

Crystal structure of human mitochondrial poly(A) polymerase (PAPD1)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	The precipitant solution contained 100 mM MES (pH 6.0), 6% (v/v) PEG4000, 35 mM NaCl, and 5 mM MgSO4. The protein was at 20 mg/mL concentration, and 0.5 mM MgATP was included as an additive., microbatch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.68	α = 90
b = 76.88	β = 103.39
c = 87.63	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 4	MIRRORS		M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.96863, 0.97888, 0.97926	NSLS	X4A

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	3.1	30	97.7	0.08	8.9681	2.4		30725

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)
	3.1	3.21	90.1		0.289	2.342	2

Refinement

Statistics
Diffraction ID	Structure Solution 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	MAD	3.1	28.912	1.37	28985	1436	91.73	0.2514	0.2473	0.2504	0.3284	0.3384	RANDOM

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]
8.9378		-12.5461	-6.8323		-3.102

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.972
f_angle_d	1.373
f_chiral_restr	0.087
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5351
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling