Experiment: 5DQO

Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L9Q	PDB entry 3L9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	300 mM lithium sulfate, 100 mM Tris, pH 8.5, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.398	α = 90
b = 60.398	β = 90
c = 246.729	γ = 120

Symmetry
Space Group	P 31

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	MARMOSAIC 300 mm CCD		2015-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0	APS	21-ID-D

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	2.3	82.243	92.5	0.058	12.8	4.5	44770	42683

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	2.48	2.53	89.6		0.493	2.1	2.9

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 (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 3L9Q	2.3	44.14	40637	2045	95.34	0.25174	0.25059	0.251	0.2749	0.2774	RANDOM	54.343

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			1.09		-2.18

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4863
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction